4YBB

High-resolution structure of the Escherichia coli ribosome

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6I7V


Literature

High-resolution structure of the Escherichia coli ribosome.

Noeske, J., Wasserman, M.R., Terry, D.S., Altman, R.B., Blanchard, S.C., Cate, J.H.

(2015) Nat Struct Mol Biol 22: 336-341

  • DOI: https://doi.org/10.1038/nsmb.2994
  • Primary Citation of Related Structures:  
    4YBB

  • PubMed Abstract: 

    • Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation have remained poorly understood. Moreover, the functions of modifications to ribosomal RNA and ribosomal proteins have also been unclear ...

    Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation have remained poorly understood. Moreover, the functions of modifications to ribosomal RNA and ribosomal proteins have also been unclear. Here we present the structure of the Escherichia coli 70S ribosome at 2.4-Å resolution. The structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and it suggests how solvation contributes to ribosome integrity and function as well as how the conformation of ribosomal protein uS12 aids in mRNA decoding. This structure helps to explain the phylogenetic conservation of key elements of the ribosome, including post-transcriptional and post-translational modifications, and should serve as a basis for future antibiotic development.

    Organizational Affiliation: 

    1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA. [2] Department of Chemistry, University of California, Berkeley, Berkeley, California, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB],
W [auth BB]		224Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsB, b0169, JW0164
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC],
X [auth BC]		206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsC, b3314, JW3276
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD],
Y [auth BD]		205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsD, ramA, b3296, JW3258
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE],
Z [auth BE]		155Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsE, spc, b3303, JW3265
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6AA [auth BF],
F [auth AF]		106Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsF, b4200, JW4158
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7BA [auth BG],
G [auth AG]		151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsG, b3341, JW3303
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8CA [auth BH],
H [auth AH]		129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsH, b3306, JW3268
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9DA [auth BI],
I [auth AI]		127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsI, b3230, JW3199
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Entity ID: 10
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30S ribosomal protein S10EA [auth BJ],
J [auth AJ]		99Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJ, nusE, b3321, JW3283
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Entity ID: 11
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30S ribosomal protein S11FA [auth BK],
K [auth AK]		117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsK, b3297, JW3259
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12GA [auth BL],
L [auth AL]		123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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Entity ID: 13
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30S ribosomal protein S13HA [auth BM],
M [auth AM]		114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsM, b3298, JW3260
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Entity ID: 14
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30S ribosomal protein S14IA [auth BN],
N [auth AN]		100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsN, b3307, JW3269
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Entity ID: 15
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30S ribosomal protein S15JA [auth BO],
O [auth AO]		88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsO, secC, b3165, JW3134
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Entity ID: 16
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30S ribosomal protein S16KA [auth BP],
P [auth AP]		82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsP, b2609, JW2590
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Entity ID: 17
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30S ribosomal protein S17LA [auth BQ],
Q [auth AQ]		80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQ, neaA, b3311, JW3273
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Entity ID: 18
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30S ribosomal protein S18MA [auth BR],
R [auth AR]		55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsR, b4202, JW4160
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Entity ID: 19
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30S ribosomal protein S19NA [auth BS],
S [auth AS]		79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsS, b3316, JW3278
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Entity ID: 20
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30S ribosomal protein S20OA [auth BT],
T [auth AT]		86Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsT, b0023, JW0022
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Entity ID: 21
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30S ribosomal protein S21PA [auth BU],
U [auth AU]		56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsU, b3065, JW3037
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2SA [auth CC],
XB [auth DC]		271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplB, b3317, JW3279
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50S ribosomal protein L3TA [auth CD]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplC, b3320, JW3282
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Entity ID: 26
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50S ribosomal protein L4UA [auth CE],
ZB [auth DE]		201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplD, eryA, b3319, JW3281
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50S ribosomal protein L5AC [auth DF],
VA [auth CF]		177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplE, b3308, JW3270
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50S ribosomal protein L6BC [auth DG],
WA [auth CG]		176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplF, b3305, JW3267
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50S ribosomal protein L9CC [auth DH],
XA [auth CH]		149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplI, b4203, JW4161
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50S ribosomal protein L11EC [auth DJ],
YA [auth CJ]		134Escherichia coli K-12Mutation(s): 0 
Gene Names: rplK, relC, b3983, JW3946
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50S ribosomal protein L13FC [auth DK],
ZA [auth CK]		142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplM, b3231, JW3200
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50S ribosomal protein L14AB [auth CL],
GC [auth DL]		123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplN, b3310, JW3272
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50S ribosomal protein L15BB [auth CM],
HC [auth DM]		144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplO, b3301, JW3263
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50S ribosomal protein L16CB [auth CN],
IC [auth DN]		136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplP, b3313, JW3275
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50S ribosomal protein L17DB [auth CO],
JC [auth DO]		125Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQ, b3294, JW3256
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50S ribosomal protein L18EB [auth CP],
KC [auth DP]		117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplR, b3304, JW3266
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Entity ID: 37
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50S ribosomal protein L19FB [auth CQ],
LC [auth DQ]		114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplS, b2606, JW2587
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50S ribosomal protein L20GB [auth CR],
MC [auth DR]		117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplT, pdzA, b1716, JW1706
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50S ribosomal protein L21HB [auth CS],
NC [auth DS]		103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplU, b3186, JW3153
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Entity ID: 40
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50S ribosomal protein L22IB [auth CT],
OC [auth DT]		110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplV, eryB, b3315, JW3277
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50S ribosomal protein L23JB [auth CU],
PC [auth DU]		93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplW, b3318, JW3280
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50S ribosomal protein L24KB [auth CV],
QC [auth DV]		102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplX, b3309, JW3271
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25LB [auth CW],
RC [auth DW]		94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplY, b2185, JW2173
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27MB [auth CX],
SC [auth DX]		76Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmA, b3185, JW3152
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28NB [auth CY],
TC [auth DY]		77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmB, b3637, JW3612
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29OB [auth CZ],
UC [auth DZ]		62Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmC, b3312, JW3274
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30PB [auth C0],
VC [auth D0]		58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmD, b3302, JW3264
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32QB [auth C1],
WC [auth D1]		56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmF, b1089, JW1075
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33RB [auth C2],
XC [auth D2]		51Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmG, b3636, JW3611
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34SB [auth C3],
YC [auth D3]		46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmH, rimA, ssaF, b3703, JW3680
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35TB [auth C4],
ZC [auth D4]		64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmI, b1717, JW1707
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36AD [auth D5],
UB [auth C5]		38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJ, b3299, JW3261
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3YB [auth DD]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplC, b3320, JW3282
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10DC [auth DI]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJ, b3985, JW3948
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA [auth AA],
V [auth BA]		1,534Escherichia coli K-12
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Entity ID: 22
MoleculeChainsLengthOrganismImage
23S rRNAQA [auth CA]2,904Escherichia coli K-12
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Entity ID: 23
MoleculeChainsLengthOrganismImage
5S rRNARA [auth CB],
WB [auth DB]		120Escherichia coli K-12
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Entity ID: 53
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23S rRNAVB [auth DA]2,903Escherichia coli K-12
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Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE
Download Ideal Coordinates CCD File 
QV [auth DA],
YU [auth DA]		PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
EW [auth DA]
GV [auth DA]
LX [auth DQ]
NX [auth DR]
QX [auth DS]
EW [auth DA],
GV [auth DA],
LX [auth DQ],
NX [auth DR],
QX [auth DS],
RH [auth BA],
SF [auth AA]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
GUN
Query on GUN
Download Ideal Coordinates CCD File 
ZV [auth DA]GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
CW [auth DA]
FW [auth DA]
NW [auth DA]
PX [auth DS]
RV [auth DA]
CW [auth DA],
FW [auth DA],
NW [auth DA],
PX [auth DS],
RV [auth DA],
UX [auth DU],
XX [auth D1],
YX [auth D3],
ZU [auth DA]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
SPD
Query on SPD
Download Ideal Coordinates CCD File 
AV [auth DA],
MW [auth DA],
UV [auth DA],
WU [auth DA]		SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
IW [auth DA]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
DV [auth DA]
DX [auth DE]
EX [auth DE]
FV [auth DA]
FX [auth DK]
DV [auth DA],
DX [auth DE],
EX [auth DE],
FV [auth DA],
FX [auth DK],
IX [auth DN],
RX [auth DS],
SV [auth DA],
SX [auth DT],
TF [auth AA],
TX [auth DT],
VV [auth DA],
YF [auth AA],
YV [auth DA]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
BG [auth AL]
GW [auth DA]
GX [auth DL]
JX [auth DP]
KX [auth DQ]
BG [auth AL],
GW [auth DA],
GX [auth DL],
JX [auth DP],
KX [auth DQ],
MV [auth DA],
NV [auth DA],
OV [auth DA],
OW [auth DA],
PW [auth DA],
ZX [auth D3]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
PUT
Query on PUT
Download Ideal Coordinates CCD File 
AW [auth DA]
BV [auth DA]
BW [auth DA]
CV [auth DA]
HW [auth DA]
AW [auth DA],
BV [auth DA],
BW [auth DA],
CV [auth DA],
HW [auth DA],
HX [auth DM],
IV [auth DA],
JW [auth DA],
KW [auth DA],
LW [auth DA],
TV [auth DA],
UF [auth AA],
VF [auth AA],
WF [auth AA],
XF [auth AA],
XU [auth DA]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AG [auth AB],
AY [auth D5],
VN [auth C5]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AX [auth DB]
BX [auth DB]
CX [auth DB]
DW [auth DA]
HV [auth DA]
AX [auth DB],
BX [auth DB],
CX [auth DB],
DW [auth DA],
HV [auth DA],
KV [auth DA],
LV [auth DA],
OX [auth DR],
VX [auth D0],
WV [auth DA],
WX [auth D1],
XV [auth DA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
ACY
Query on ACY
Download Ideal Coordinates CCD File 
EV [auth DA],
JV [auth DA],
PV [auth DA]		ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AE [auth AA]
AF [auth AA]
AH [auth BA]
AI [auth CA]
AJ [auth CA]
AE [auth AA],
AF [auth AA],
AH [auth BA],
AI [auth CA],
AJ [auth CA],
AK [auth CA],
AL [auth CA],
AM [auth CA],
AN [auth CA],
AO [auth DA],
AP [auth DA],
AQ [auth DA],
AR [auth DA],
AS [auth DA],
AT [auth DA],
AU [auth DA],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BH [auth BA],
BI [auth CA],
BJ [auth CA],
BK [auth CA],
BL [auth CA],
BM [auth CA],
BN [auth CA],
BO [auth DA],
BP [auth DA],
BQ [auth DA],
BR [auth DA],
BS [auth DA],
BT [auth DA],
BU [auth DA],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth BA],
CH [auth BA],
CI [auth CA],
CJ [auth CA],
CK [auth CA],
CL [auth CA],
CM [auth CA],
CN [auth CA],
CO [auth DA],
CP [auth DA],
CQ [auth DA],
CR [auth DA],
CS [auth DA],
CT [auth DA],
CU [auth DA],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth BA],
DH [auth BA],
DI [auth CA],
DJ [auth CA],
DK [auth CA],
DL [auth CA],
DM [auth CA],
DN [auth CA],
DO [auth DA],
DP [auth DA],
DQ [auth DA],
DR [auth DA],
DS [auth DA],
DT [auth DA],
DU [auth DA],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth BA],
EH [auth BA],
EI [auth CA],
EJ [auth CA],
EK [auth CA],
EL [auth CA],
EM [auth CA],
EN [auth CA],
EO [auth DA],
EP [auth DA],
EQ [auth DA],
ER [auth DA],
ES [auth DA],
ET [auth DA],
EU [auth DA],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth BA],
FH [auth BA],
FI [auth CA],
FJ [auth CA],
FK [auth CA],
FL [auth CA],
FM [auth CA],
FN [auth CA],
FO [auth DA],
FP [auth DA],
FQ [auth DA],
FR [auth DA],
FS [auth DA],
FT [auth DA],
FU [auth DA],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth BA],
GH [auth BA],
GI [auth CA],
GJ [auth CA],
GK [auth CA],
GL [auth CA],
GM [auth CA],
GN [auth CA],
GO [auth DA],
GP [auth DA],
GQ [auth DA],
GR [auth DA],
GS [auth DA],
GT [auth DA],
GU [auth DA],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth BA],
HH [auth BA],
HI [auth CA],
HJ [auth CA],
HK [auth CA],
HL [auth CA],
HM [auth CA],
HN [auth CA],
HO [auth DA],
HP [auth DA],
HQ [auth DA],
HR [auth DA],
HS [auth DA],
HT [auth DA],
HU [auth DA],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth BA],
IH [auth BA],
II [auth CA],
IJ [auth CA],
IK [auth CA],
IL [auth CA],
IM [auth CA],
IN [auth CA],
IO [auth DA],
IP [auth DA],
IQ [auth DA],
IR [auth DA],
IS [auth DA],
IT [auth DA],
IU [auth DA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth BA],
JH [auth BA],
JI [auth CA],
JJ [auth CA],
JK [auth CA],
JL [auth CA],
JM [auth CA],
JN [auth CA],
JO [auth DA],
JP [auth DA],
JQ [auth DA],
JR [auth DA],
JS [auth DA],
JT [auth DA],
JU [auth DA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth BA],
KH [auth BA],
KI [auth CA],
KJ [auth CA],
KK [auth CA],
KL [auth CA],
KM [auth CA],
KN [auth CA],
KO [auth DA],
KP [auth DA],
KQ [auth DA],
KR [auth DA],
KS [auth DA],
KT [auth DA],
KU [auth DA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth BA],
LH [auth BA],
LI [auth CA],
LJ [auth CA],
LK [auth CA],
LL [auth CA],
LM [auth CA],
LN [auth CA],
LO [auth DA],
LP [auth DA],
LQ [auth DA],
LR [auth DA],
LS [auth DA],
LT [auth DA],
LU [auth DA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
MG [auth BA],
MH [auth BA],
MI [auth CA],
MJ [auth CA],
MK [auth CA],
ML [auth CA],
MM [auth CA],
MN [auth CA],
MO [auth DA],
MP [auth DA],
MQ [auth DA],
MR [auth DA],
MS [auth DA],
MT [auth DA],
MU [auth DA],
MX [auth DR],
ND [auth AA],
NE [auth AA],
NF [auth AA],
NG [auth BA],
NH [auth BA],
NI [auth CA],
NJ [auth CA],
NK [auth CA],
NL [auth CA],
NM [auth CA],
NN [auth CA],
NO [auth DA],
NP [auth DA],
NQ [auth DA],
NR [auth DA],
NS [auth DA],
NT [auth DA],
NU [auth DA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
OG [auth BA],
OH [auth BA],
OI [auth CA],
OJ [auth CA],
OK [auth CA],
OL [auth CA],
OM [auth CA],
ON [auth CA],
OO [auth DA],
OP [auth DA],
OQ [auth DA],
OR [auth DA],
OS [auth DA],
OT [auth DA],
OU [auth DA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
PG [auth BA],
PH [auth BA],
PI [auth CA],
PJ [auth CA],
PK [auth CA],
PL [auth CA],
PM [auth CA],
PN [auth CA],
PO [auth DA],
PP [auth DA],
PQ [auth DA],
PR [auth DA],
PS [auth DA],
PT [auth DA],
PU [auth DA],
QD [auth AA],
QE [auth AA],
QF [auth AA],
QG [auth BA],
QH [auth BA],
QI [auth CA],
QJ [auth CA],
QK [auth CA],
QL [auth CA],
QM [auth CA],
QN [auth CA],
QO [auth DA],
QP [auth DA],
QQ [auth DA],
QR [auth DA],
QS [auth DA],
QT [auth DA],
QU [auth DA],
QW [auth DA],
RD [auth AA],
RE [auth AA],
RF [auth AA],
RG [auth BA],
RI [auth CA],
RJ [auth CA],
RK [auth CA],
RL [auth CA],
RM [auth CA],
RN [auth CB],
RO [auth DA],
RP [auth DA],
RQ [auth DA],
RR [auth DA],
RS [auth DA],
RT [auth DA],
RU [auth DA],
RW [auth DB],
SD [auth AA],
SE [auth AA],
SG [auth BA],
SH [auth CA],
SI [auth CA],
SJ [auth CA],
SK [auth CA],
SL [auth CA],
SM [auth CA],
SN [auth CB],
SO [auth DA],
SP [auth DA],
SQ [auth DA],
SR [auth DA],
SS [auth DA],
ST [auth DA],
SU [auth DA],
SW [auth DB],
TD [auth AA],
TE [auth AA],
TG [auth BA],
TH [auth CA],
TI [auth CA],
TJ [auth CA],
TK [auth CA],
TL [auth CA],
TM [auth CA],
TN [auth CB],
TO [auth DA],
TP [auth DA],
TQ [auth DA],
TR [auth DA],
TS [auth DA],
TT [auth DA],
TU [auth DA],
TW [auth DB],
UD [auth AA],
UE [auth AA],
UG [auth BA],
UH [auth CA],
UI [auth CA],
UJ [auth CA],
UK [auth CA],
UL [auth CA],
UM [auth CA],
UN [auth C3],
UO [auth DA],
UP [auth DA],
UQ [auth DA],
UR [auth DA],
US [auth DA],
UT [auth DA],
UU [auth DA],
UW [auth DB],
VD [auth AA],
VE [auth AA],
VG [auth BA],
VH [auth CA],
VI [auth CA],
VJ [auth CA],
VK [auth CA],
VL [auth CA],
VM [auth CA],
VO [auth DA],
VP [auth DA],
VQ [auth DA],
VR [auth DA],
VS [auth DA],
VT [auth DA],
VU [auth DA],
VW [auth DB],
WD [auth AA],
WE [auth AA],
WG [auth BA],
WH [auth CA],
WI [auth CA],
WJ [auth CA],
WK [auth CA],
WL [auth CA],
WM [auth CA],
WN [auth DA],
WO [auth DA],
WP [auth DA],
WQ [auth DA],
WR [auth DA],
WS [auth DA],
WT [auth DA],
WW [auth DB],
XD [auth AA],
XE [auth AA],
XG [auth BA],
XH [auth CA],
XI [auth CA],
XJ [auth CA],
XK [auth CA],
XL [auth CA],
XM [auth CA],
XN [auth DA],
XO [auth DA],
XP [auth DA],
XQ [auth DA],
XR [auth DA],
XS [auth DA],
XT [auth DA],
XW [auth DB],
YD [auth AA],
YE [auth AA],
YG [auth BA],
YH [auth CA],
YI [auth CA],
YJ [auth CA],
YK [auth CA],
YL [auth CA],
YM [auth CA],
YN [auth DA],
YO [auth DA],
YP [auth DA],
YQ [auth DA],
YR [auth DA],
YS [auth DA],
YT [auth DA],
YW [auth DB],
ZD [auth AA],
ZE [auth AA],
ZF [auth AA],
ZG [auth BA],
ZH [auth CA],
ZI [auth CA],
ZJ [auth CA],
ZK [auth CA],
ZL [auth CA],
ZM [auth CA],
ZN [auth DA],
ZO [auth DA],
ZP [auth DA],
ZQ [auth DA],
ZR [auth DA],
ZS [auth DA],
ZT [auth DA],
ZW [auth DB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
D2T
Query on D2T		GA [auth BL],
L [auth AL]		L-PEPTIDE LINKINGC5 H9 N O4 SASP
4D4
Query on 4D4		CB [auth CN],
IC [auth DN]		L-PEPTIDE LINKINGC6 H14 N4 O3ARG
MEQ
Query on MEQ		YB [auth DD]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.17α = 90
b = 433.89β = 90
c = 624.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references