4ZER

Crystal structure of the Onc112 antimicrobial peptide bound to the Thermus thermophilus 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex.

Seefeldt, A.C.Nguyen, F.Antunes, S.Perebaskine, N.Graf, M.Arenz, S.Inampudi, K.K.Douat, C.Guichard, G.Wilson, D.N.Innis, C.A.

(2015) Nat.Struct.Mol.Biol. 22: 470-475

  • DOI: 10.1038/nsmb.3034

  • PubMed Abstract: 
  • The increasing prevalence of multidrug-resistant pathogenic bacteria is making current antibiotics obsolete. Proline-rich antimicrobial peptides (PrAMPs) display potent activity against Gram-negative bacteria and thus represent an avenue for antibiot ...

    The increasing prevalence of multidrug-resistant pathogenic bacteria is making current antibiotics obsolete. Proline-rich antimicrobial peptides (PrAMPs) display potent activity against Gram-negative bacteria and thus represent an avenue for antibiotic development. PrAMPs from the oncocin family interact with the ribosome to inhibit translation, but their mode of action has remained unclear. Here we have determined a structure of the Onc112 peptide in complex with the Thermus thermophilus 70S ribosome at a resolution of 3.1 Å by X-ray crystallography. The Onc112 peptide binds within the ribosomal exit tunnel and extends toward the peptidyl transferase center, where it overlaps with the binding site for an aminoacyl-tRNA. We show biochemically that the binding of Onc112 blocks and destabilizes the initiation complex, thus preventing entry into the elongation phase. Our findings provide a basis for the future development of this class of potent antimicrobial agents.


    Organizational Affiliation

    1] Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France. [2] INSERM U869, Bordeaux, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
1D, 2D
275Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplB
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
1E, 2E
204Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I04
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
1F, 2F
203Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
1G, 2G
181Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
1H, 2H
174Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I19
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
1I, 2I
147Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
1N, 2N
140Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
1O, 2O
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
1P, 2P
149Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I23
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
1Q, 2Q
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
1R, 2R
118Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
1S, 2S
110Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I20
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
1T, 2T
131Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
1U, 2U
116Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
1V, 2V
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
1W, 2W
112Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I09
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
1X, 2X
95Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I06
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
1Y, 2Y
107Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I15
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
1Z, 2Z
203Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
10, 20
77Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
11, 21
97Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
12, 22
70Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
13, 23
59Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I22
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
14, 24
69Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
15, 25
59Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
16, 26
53Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmG
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
17, 27
48Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
18, 28
64Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L77
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
19, 29
37Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q72I28 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I28
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
1b, 2b
231Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
1c, 2c
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
1d, 2d
208Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
1e, 2e
148Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsE (rps5)
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
1f, 2f
100Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsF (rps6)
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62666
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
1g, 2g
155Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
1h, 2h
137Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsH (rps8)
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62668
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
1i, 2i
127Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
1j, 2j
97Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsJ (rps10)
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62653
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
1k, 2k
114Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
1l, 2l
122Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsL (rps12)
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
1m, 2m
116Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
1n, 2n
60Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsZ (rps14, rpsN)
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62656
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
1o, 2o
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsO (rps15)
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62657
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
1p, 2p
82Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
1q, 2q
99Thermus aquaticusMutation(s): 0 
Gene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
1r, 2r
68Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
1s, 2s
83Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsS (rps19)
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62660
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
1t, 2t
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
1u, 2u
23Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Onc112
1y, 2y
19N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
23s ribosomal RNA1A,2A2915Thermus thermophilus HB8
Entity ID: 2
MoleculeChainsLengthOrganism
5s ribosomal RNA1B,2B120Thermus thermophilus HB8
Entity ID: 32
MoleculeChainsLengthOrganism
16s ribosomal RNA1a,2a1521Thermus thermophilus HB8
Entity ID: 53
MoleculeChainsLengthOrganism
tRNA met1x,2x76Escherichia coli K-12
Entity ID: 55
MoleculeChainsLengthOrganism
mRNAA,B27Thermus thermophilus HB8
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
2A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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Download CCD File 
1d, 2d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
14, 15, 16, 19, 1n, 1Y, 24, 25, 26, 29, 2n, 2Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
1A, 2A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
MG
Query on MG

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10, 11, 13, 15, 17, 18, 19, 1a, 1A, 1b, 1B, 1d, 1D, 1E, 1e, 1f, 1F, 1g, 1G, 1H, 1i, 1l, 1n, 1N, 1o, 1O, 1P, 1Q, 1r, 1R, 1t, 1T, 1U, 1V, 1W, 1X, 1x, 1Y, 1Z, 20, 21, 23, 28, 2A, 2a, 2B, 2D, 2e, 2E, 2f, 2F, 2G, 2I, 2j, 2k, 2l, 2n, 2N, 2O, 2p, 2P, 2Q, 2q, 2R, 2t, 2T, 2U, 2V, 2W, 2x, 2X, 2Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
1B
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
1A, 1a
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  15 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1a, 1A, 1x, 2a, 2A, 2x
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
1A, 1a, 1x, 2A, 2a, 2x
RNA LINKINGC10 H16 N3 O8 PC
OMU
Query on OMU
1A, 2A
RNA LINKINGC10 H15 N2 O9 PU
M2G
Query on M2G
1a, 2a
RNA LINKINGC12 H18 N5 O8 PG
OMC
Query on OMC
1A, 2A
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
1a, 2a
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
1x, 2x
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
1a, 2a
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
1a, 2a
RNA LINKINGC11 H17 N5 O8 PG
UR3
Query on UR3
1a, 2a
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
1A, 2A
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
1A, 1x, 2A, 2x
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
1A, 2A
RNA LINKINGC11 H16 N5 O7 PA
0TD
Query on 0TD
1l, 2l
L-PEPTIDE LINKINGC5 H9 N O4 SASP
4OC
Query on 4OC
1a, 2a
RNA LINKINGC11 H18 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 209.300α = 90.00
b = 452.290β = 90.00
c = 625.120γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references
  • Version 1.2: 2015-06-10
    Type: Database references
  • Version 1.3: 2016-01-13
    Type: Structure summary
  • Version 1.4: 2016-03-23
    Type: Structure summary
  • Version 1.5: 2017-10-18
    Type: Data collection