4P6F

Crystal structure of the peptolide 12C bound to bacterial ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Macrolide-Peptide Conjugates as Probes of the Path of Travel of the Nascent Peptides through the Ribosome.

Washington, A.Z.Benicewicz, D.B.Canzoneri, J.C.Fagan, C.E.Mwakwari, S.C.Maehigashi, T.Dunham, C.M.Oyelere, A.K.

(2014) ACS Chem Biol 9: 2621-2631

  • DOI: 10.1021/cb5003224
  • Primary Citation of Related Structures:  
    4P6F

  • PubMed Abstract: 
  • Despite decades of research on the bacterial ribosome, the ribosomal exit tunnel is still poorly understood. Although it has been suggested that the exit tunnel is simply a convenient route of egress for the nascent chain, specific protein sequences serve to slow the rate of translation, suggesting some degree of interaction between the nascent peptide chain and the exit tunnel ...

    Despite decades of research on the bacterial ribosome, the ribosomal exit tunnel is still poorly understood. Although it has been suggested that the exit tunnel is simply a convenient route of egress for the nascent chain, specific protein sequences serve to slow the rate of translation, suggesting some degree of interaction between the nascent peptide chain and the exit tunnel. To understand how the ribosome interacts with nascent peptide sequences, we synthesized and characterized a novel class of probe molecules. These peptide-macrolide (or "peptolide") conjugates were designed to present unique peptide sequences to the exit tunnel. Biochemical and X-ray structural analyses of the interactions between these probes and the ribosome reveal interesting insights about the exit tunnel. Using translation inhibition and RNA structure probing assays, we find the exit tunnel has a relaxed preference for the directionality (N → C or C → N orientation) of the nascent peptides. Moreover, the X-ray crystal structure of one peptolide derived from a positively charged, reverse Nuclear Localization Sequence peptide, bound to the 70S bacterial ribosome, reveals that the macrolide ring of the peptolide binds in the same position as other macrolides. However, the peptide tail folds over the macrolide ring, oriented toward the peptidyl transferase center and interacting in a novel manner with 23S rRNA residue C2442 and His69 of ribosomal protein L4. These data suggest that these peptolides are viable probes for interrogating nascent peptide-exit tunnel interaction.


    Organizational Affiliation

    School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth QB], GB [auth XB]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth QC], HB [auth XC]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth QD], IB [auth XD]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth QE], JB [auth XE]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth QF], KB [auth XF]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth QG], LB [auth XG]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth QH], MB [auth XH]138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth QI], NB [auth XI]128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth QJ], OB [auth XJ]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth QK], PB [auth XK]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth QL], QB [auth XL]132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth QM], RB [auth XM]126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth QN], SB [auth XN]61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth QO], TB [auth XO]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth QP], UB [auth XP]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth QQ], VB [auth XQ]105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth QR], WB [auth XR]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth QS], XB [auth XS]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth QT], YB [auth XT]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth QU], ZB [auth XU]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2BA [auth RD], GC [auth YD]276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3CA [auth RE], HC [auth YE]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4DA [auth RF], IC [auth YF]210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5EA [auth RG], JC [auth YG]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth RH], KC [auth YH]180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9GA [auth RI], LC [auth YI]148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth RN], MC [auth YN]140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth RO], NC [auth YO]122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth RP], OC [auth YP]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16KA [auth RQ], PC [auth YQ]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17LA [auth RR], QC [auth YR]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18MA [auth RS], RC [auth YS]112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19NA [auth RT], SC [auth YT]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20OA [auth RU], TC [auth YU]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21PA [auth RV], UC [auth YV]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22QA [auth RW], VC [auth YW]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23RA [auth RX], WC [auth YX]96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24SA [auth RY], XC [auth YY]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25TA [auth RZ], YC [auth YZ]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27UA [auth R0], ZC [auth Y0]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28VA [auth R1], AD [auth Y1]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29WA [auth R2], BD [auth Y2]72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30XA [auth R3], CD [auth Y3]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31YA [auth R4], DD [auth Y4]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32ZA [auth R5], ED [auth Y5]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33AB [auth R6], FD [auth Y6]54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34BB [auth R7], GD [auth Y7]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35CB [auth R8], HD [auth Y8]65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36DB [auth R9], ID [auth Y9]37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q5SHR2
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
T17-GLY-GLY-PRO-LYS-LYS-LYS-LYS-LYS-VAL-GLY-GLYEB [auth Z7], JD [auth Z8]12synthetic constructMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth QA], FB [auth XA]1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
tRNA-fMetV [auth QV], AC [auth XV]77Escherichia coli str. K-12 substr. MG1655
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Entity ID: 23
MoleculeChainsLengthOrganismImage
E-Site tRNA-Phe or A-Site tRNA-PheW [auth QW], Y [auth QY], BC [auth XW], DC [auth XY]76Escherichia coli str. K-12 substr. MG1655
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Entity ID: 24
MoleculeChainsLengthOrganismImage
mRNAX [auth QX], CC [auth XX]24Thermus thermophilus HB8
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Entity ID: 25
MoleculeChainsLengthOrganismImage
23S ribosomal RNAZ [auth RA], EC [auth YA]2915Thermus thermophilus HB8
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Entity ID: 26
MoleculeChainsLengthOrganismImage
5S ribosomal RNAAA [auth RB], FC [auth YB]122Thermus thermophilus HB8
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
XS [auth XA], YF [auth QA]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AG [auth QD], BT [auth XN], DG [auth QN], DQ [auth R5], LEA [auth Y9], ZS [auth XD]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AAA [auth YA] , ABA [auth YA] , ACA [auth YA] , ADA [auth YA] , AE [auth QA] , AEA [auth YB] , AF [auth QA] , AH [auth RA] , 
AAA [auth YA],  ABA [auth YA],  ACA [auth YA],  ADA [auth YA],  AE [auth QA],  AEA [auth YB],  AF [auth QA],  AH [auth RA],  AI [auth RA],  AJ [auth RA],  AK [auth RA],  AL [auth RA],  AM [auth RA],  AN [auth RA],  AO [auth RA],  AP [auth RA],  AQ [auth RP],  AR [auth XA],  AS [auth XA],  AT [auth XM],  AU [auth YA],  AV [auth YA],  AW [auth YA],  AX [auth YA],  AY [auth YA],  AZ [auth YA],  BAA [auth YA],  BBA [auth YA],  BCA [auth YA],  BDA [auth YA],  BE [auth QA],  BEA [auth YB],  BF [auth QA],  BG [auth QF],  BH [auth RA],  BI [auth RA],  BJ [auth RA],  BK [auth RA],  BL [auth RA],  BM [auth RA],  BN [auth RA],  BO [auth RA],  BP [auth RA],  BQ [auth R0],  BR [auth XA],  BS [auth XA],  BU [auth YA],  BV [auth YA],  BW [auth YA],  BX [auth YA],  BY [auth YA],  BZ [auth YA],  CAA [auth YA],  CBA [auth YA],  CCA [auth YA],  CDA [auth YA],  CE [auth QA],  CEA [auth YB],  CF [auth QA],  CG [auth QH],  CH [auth RA],  CI [auth RA],  CJ [auth RA],  CK [auth RA],  CL [auth RA],  CM [auth RA],  CN [auth RA],  CO [auth RA],  CP [auth RA],  CQ [auth R5],  CR [auth XA],  CS [auth XA],  CT [auth XV],  CU [auth YA],  CV [auth YA],  CW [auth YA],  CX [auth YA],  CY [auth YA],  CZ [auth YA],  DAA [auth YA],  DBA [auth YA],  DCA [auth YA],  DDA [auth YA],  DE [auth QA],  DEA [auth YB],  DF [auth QA],  DH [auth RA],  DI [auth RA],  DJ [auth RA],  DK [auth RA],  DL [auth RA],  DM [auth RA],  DN [auth RA],  DO [auth RA],  DP [auth RA],  DR [auth XA],  DS [auth XA],  DT [auth XV],  DU [auth YA],  DV [auth YA],  DW [auth YA],  DX [auth YA],  DY [auth YA],  DZ [auth YA],  EAA [auth YA],  EBA [auth YA],  ECA [auth YA],  EDA [auth YA],  EE [auth QA],  EEA [auth YD],  EF [auth QA],  EG [auth QV],  EH [auth RA],  EI [auth RA],  EJ [auth RA],  EK [auth RA],  EL [auth RA],  EM [auth RA],  EN [auth RA],  EO [auth RA],  EP [auth RA],  EQ [auth XA],  ER [auth XA],  ES [auth XA],  ET [auth XV],  EU [auth YA],  EV [auth YA],  EW [auth YA],  EX [auth YA],  EY [auth YA],  EZ [auth YA],  FAA [auth YA],  FBA [auth YA],  FCA [auth YA],  FDA [auth YA],  FE [auth QA],  FEA [auth YE],  FF [auth QA],  FG [auth QV],  FH [auth RA],  FI [auth RA],  FJ [auth RA],  FK [auth RA],  FL [auth RA],  FM [auth RA],  FN [auth RA],  FO [auth RA],  FP [auth RA],  FQ [auth XA],  FR [auth XA],  FS [auth XA],  FT [auth XX],  FU [auth YA],  FV [auth YA],  FW [auth YA],  FX [auth YA],  FY [auth YA],  FZ [auth YA],  GAA [auth YA],  GBA [auth YA],  GCA [auth YA],  GDA [auth YA],  GE [auth QA],  GEA [auth YE],  GF [auth QA],  GG [auth QY],  GH [auth RA],  GI [auth RA],  GJ [auth RA],  GK [auth RA],  GL [auth RA],  GM [auth RA],  GN [auth RA],  GO [auth RA],  GP [auth RA],  GQ [auth XA],  GR [auth XA],  GS [auth XA],  GT [auth XY],  GU [auth YA],  GV [auth YA],  GW [auth YA],  GX [auth YA],  GY [auth YA],  GZ [auth YA],  HAA [auth YA],  HBA [auth YA],  HCA [auth YA],  HDA [auth YA],  HE [auth QA],  HEA [auth YP],  HF [auth QA],  HG [auth RA],  HH [auth RA],  HI [auth RA],  HJ [auth RA],  HK [auth RA],  HL [auth RA],  HM [auth RA],  HN [auth RA],  HO [auth RA],  HP [auth RA],  HQ [auth XA],  HR [auth XA],  HS [auth XA],  HT [auth YA],  HU [auth YA],  HV [auth YA],  HW [auth YA],  HX [auth YA],  HY [auth YA],  HZ [auth YA],  IAA [auth YA],  IBA [auth YA],  ICA [auth YA],  IDA [auth YA],  IE [auth QA],  IEA [auth YX],  IF [auth QA],  IG [auth RA],  IH [auth RA],  II [auth RA],  IJ [auth RA],  IK [auth RA],  IL [auth RA],  IM [auth RA],  IN [auth RA],  IO [auth RA],  IP [auth RA],  IQ [auth XA],  IR [auth XA],  IS [auth XA],  IT [auth YA],  IU [auth YA],  IV [auth YA],  IW [auth YA],  IX [auth YA],  IY [auth YA],  IZ [auth YA],  JAA [auth YA],  JBA [auth YA],  JCA [auth YA],  JDA [auth YA],  JE [auth QA],  JEA [auth Y5],  JF [auth QA],  JG [auth RA],  JH [auth RA],  JI [auth RA],  JJ [auth RA],  JK [auth RA],  JL [auth RA],  JM [auth RA],  JN [auth RA],  JO [auth RA],  JP [auth RA],  JQ [auth XA],  JR [auth XA],  JS [auth XA],  JT [auth YA],  JU [auth YA],  JV [auth YA],  JW [auth YA],  JX [auth YA],  JY [auth YA],  JZ [auth YA],  KAA [auth YA],  KBA [auth YA],  KCA [auth YA],  KD [auth QA],  KDA [auth YA],  KE [auth QA],  KEA [auth Y7],  KF [auth QA],  KG [auth RA],  KH [auth RA],  KI [auth RA],  KJ [auth RA],  KK [auth RA],  KL [auth RA],  KM [auth RA],  KN [auth RA],  KO [auth RA],  KP [auth RA],  KQ [auth XA],  KR [auth XA],  KS [auth XA],  KT [auth YA],  KU [auth YA],  KV [auth YA],  KW [auth YA],  KX [auth YA],  KY [auth YA],  KZ [auth YA],  LAA [auth YA],  LBA [auth YA],  LCA [auth YA],  LD [auth QA],  LDA [auth YA],  LE [auth QA],  LF [auth QA],  LG [auth RA],  LH [auth RA],  LI [auth RA],  LJ [auth RA],  LK [auth RA],  LL [auth RA],  LM [auth RA],  LN [auth RA],  LO [auth RA],  LP [auth RA],  LQ [auth XA],  LR [auth XA],  LS [auth XA],  LT [auth YA],  LU [auth YA],  LV [auth YA],  LW [auth YA],  LX [auth YA],  LY [auth YA],  LZ [auth YA],  MAA [auth YA],  MBA [auth YA],  MCA [auth YA],  MD [auth QA],  MDA [auth YA],  ME [auth QA],  MF [auth QA],  MG [auth RA],  MH [auth RA],  MI [auth RA],  MJ [auth RA],  MK [auth RA],  ML [auth RA],  MM [auth RA],  MN [auth RA],  MO [auth RA],  MP [auth RA],  MQ [auth XA],  MR [auth XA],  MS [auth XA],  MT [auth YA],  MU [auth YA],  MV [auth YA],  MW [auth YA],  MX [auth YA],  MY [auth YA],  MZ [auth YA],  NAA [auth YA],  NBA [auth YA],  NCA [auth YA],  ND [auth QA],  NDA [auth YA],  NE [auth QA],  NF [auth QA],  NG [auth RA],  NH [auth RA],  NI [auth RA],  NJ [auth RA],  NK [auth RA],  NL [auth RA],  NM [auth RA],  NN [auth RA],  NO [auth RA],  NP [auth RA],  NQ [auth XA],  NR [auth XA],  NS [auth XA],  NT [auth YA],  NU [auth YA],  NV [auth YA],  NW [auth YA],  NX [auth YA],  NY [auth YA],  NZ [auth YA],  OAA [auth YA],  OBA [auth YA],  OCA [auth YA],  OD [auth QA],  ODA [auth YA],  OE [auth QA],  OF [auth QA],  OG [auth RA],  OH [auth RA],  OI [auth RA],  OJ [auth RA],  OK [auth RA],  OL [auth RA],  OM [auth RA],  ON [auth RA],  OO [auth RA],  OP [auth RA],  OQ [auth XA],  OR [auth XA],  OS [auth XA],  OT [auth YA],  OU [auth YA],  OV [auth YA],  OW [auth YA],  OX [auth YA],  OY [auth YA],  OZ [auth YA],  PAA [auth YA],  PBA [auth YA],  PCA [auth YA],  PD [auth QA],  PDA [auth YA],  PE [auth QA],  PF [auth QA],  PG [auth RA],  PH [auth RA],  PI [auth RA],  PJ [auth RA],  PK [auth RA],  PL [auth RA],  PM [auth RA],  PN [auth RA],  PO [auth RA],  PP [auth RA],  PQ [auth XA],  PR [auth XA],  PS [auth XA],  PT [auth YA],  PU [auth YA],  PV [auth YA],  PW [auth YA],  PX [auth YA],  PY [auth YA],  PZ [auth YA],  QAA [auth YA],  QBA [auth YA],  QCA [auth YA],  QD [auth QA],  QDA [auth YA],  QE [auth QA],  QF [auth QA],  QG [auth RA],  QH [auth RA],  QI [auth RA],  QJ [auth RA],  QK [auth RA],  QL [auth RA],  QM [auth RA],  QN [auth RA],  QO [auth RA],  QP [auth RA],  QQ [auth XA],  QR [auth XA],  QS [auth XA],  QT [auth YA],  QU [auth YA],  QV [auth YA],  QW [auth YA],  QX [auth YA],  QY [auth YA],  QZ [auth YA],  RAA [auth YA],  RBA [auth YA],  RCA [auth YA],  RD [auth QA],  RDA [auth YA],  RE [auth QA],  RF [auth QA],  RG [auth RA],  RH [auth RA],  RI [auth RA],  RJ [auth RA],  RK [auth RA],  RL [auth RA],  RM [auth RA],  RN [auth RA],  RO [auth RA],  RP [auth RA],  RQ [auth XA],  RR [auth XA],  RS [auth XA],  RT [auth YA],  RU [auth YA],  RV [auth YA],  RW [auth YA],  RX [auth YA],  RY [auth YA],  RZ [auth YA],  SAA [auth YA],  SBA [auth YA],  SCA [auth YA],  SD [auth QA],  SDA [auth YA],  SE [auth QA],  SF [auth QA],  SG [auth RA],  SH [auth RA],  SI [auth RA],  SJ [auth RA],  SK [auth RA],  SL [auth RA],  SM [auth RA],  SN [auth RA],  SO [auth RA],  SP [auth RA],  SQ [auth XA],  SR [auth XA],  SS [auth XA],  ST [auth YA],  SU [auth YA],  SV [auth YA],  SW [auth YA],  SX [auth YA],  SY [auth YA],  SZ [auth YA],  TAA [auth YA],  TBA [auth YA],  TCA [auth YA],  TD [auth QA],  TDA [auth YA],  TE [auth QA],  TF [auth QA],  TG [auth RA],  TH [auth RA],  TI [auth RA],  TJ [auth RA],  TK [auth RA],  TL [auth RA],  TM [auth RA],  TN [auth RA],  TO [auth RA],  TP [auth RB],  TQ [auth XA],  TR [auth XA],  TS [auth XA],  TT [auth YA],  TU [auth YA],  TV [auth YA],  TW [auth YA],  TX [auth YA],  TY [auth YA],  TZ [auth YA],  UAA [auth YA],  UBA [auth YA],  UCA [auth YA],  UD [auth QA],  UDA [auth YA],  UE [auth QA],  UF [auth QA],  UG [auth RA],  UH [auth RA],  UI [auth RA],  UJ [auth RA],  UK [auth RA],  UL [auth RA],  UM [auth RA],  UN [auth RA],  UO [auth RA],  UP [auth RB],  UQ [auth XA],  UR [auth XA],  US [auth XA],  UT [auth YA],  UU [auth YA],  UV [auth YA],  UW [auth YA],  UX [auth YA],  UY [auth YA],  UZ [auth YA],  VAA [auth YA],  VBA [auth YA],  VCA [auth YA],  VD [auth QA],  VDA [auth YA],  VE [auth QA],  VF [auth QA],  VG [auth RA],  VH [auth RA],  VI [auth RA],  VJ [auth RA],  VK [auth RA],  VL [auth RA],  VM [auth RA],  VN [auth RA],  VO [auth RA],  VP [auth RD],  VQ [auth XA],  VR [auth XA],  VS [auth XA],  VT [auth YA],  VU [auth YA],  VV [auth YA],  VW [auth YA],  VX [auth YA],  VY [auth YA],  VZ [auth YA],  WAA [auth YA],  WBA [auth YA],  WCA [auth YA],  WD [auth QA],  WDA [auth YA],  WE [auth QA],  WF [auth QA],  WG [auth RA],  WH [auth RA],  WI [auth RA],  WJ [auth RA],  WK [auth RA],  WL [auth RA],  WM [auth RA],  WN [auth RA],  WO [auth RA],  WP [auth RE],  WQ [auth XA],  WR [auth XA],  WS [auth XA],  WT [auth YA],  WU [auth YA],  WV [auth YA],  WW [auth YA],  WX [auth YA],  WY [auth YA],  WZ [auth YA],  XAA [auth YA],  XBA [auth YA],  XCA [auth YA],  XD [auth QA],  XDA [auth YA],  XE [auth QA],  XF [auth QA],  XG [auth RA],  XH [auth RA],  XI [auth RA],  XJ [auth RA],  XK [auth RA],  XL [auth RA],  XM [auth RA],  XN [auth RA],  XO [auth RA],  XP [auth RP],  XQ [auth XA],  XR [auth XA],  XT [auth YA],  XU [auth YA],  XV [auth YA],  XW [auth YA],  XX [auth YA],  XY [auth YA],  XZ [auth YA],  YAA [auth YA],  YBA [auth YA],  YCA [auth YA],  YD [auth QA],  YDA [auth YA],  YE [auth QA],  YG [auth RA],  YH [auth RA],  YI [auth RA],  YJ [auth RA],  YK [auth RA],  YL [auth RA],  YM [auth RA],  YN [auth RA],  YO [auth RA],  YP [auth RP],  YQ [auth XA],  YR [auth XA],  YS [auth XB],  YT [auth YA],  YU [auth YA],  YV [auth YA],  YW [auth YA],  YX [auth YA],  YY [auth YA],  YZ [auth YA],  ZAA [auth YA],  ZBA [auth YA],  ZCA [auth YA],  ZD [auth QA],  ZDA [auth YB],  ZE [auth QA],  ZF [auth QA],  ZG [auth RA],  ZH [auth RA],  ZI [auth RA],  ZJ [auth RA],  ZK [auth RA],  ZL [auth RA],  ZM [auth RA],  ZN [auth RA],  ZO [auth RA],  ZP [auth RP],  ZQ [auth XA],  ZR [auth XA],  ZT [auth YA],  ZU [auth YA],  ZV [auth YA],  ZW [auth YA],  ZX [auth YA],  ZY [auth YA],  ZZ [auth YA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.24α = 90
b = 443.46β = 90
c = 618.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM093279

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2014-12-10
    Changes: Other
  • Version 1.3: 2015-09-30
    Changes: Data collection
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence