SMTL ID : 8c1n.1

FMDV 3D polymerase in complex with 3B1 protein solved in P212121 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-1-mer

Ligands

2 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.1: 5 residues within 4Å: Chain A: R.168, K.172, Y.241, S.242, A.243 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.243 Salt bridges: A:R.168, A:R.168, A:K.172, A:K.172, A:K.177 3PO.7: 5 residues within 4Å: Chain B: R.168, K.172, Y.241, S.242, A.243 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.243 Salt bridges: B:R.168, B:K.172, B:K.172, B:K.172

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: W.237, D.238, P.366, A.367, D.368, F.374, V.375, H.378 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.238, A:A.367, A:D.368, A:V.375, A:V.375 GOL.3: 6 residues within 4Å: Chain A: K.71, R.75, D.251, N.254, I.255, E.258 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.258 Water bridges: A:K.65, A:K.71, A:D.251, A:N.254 GOL.4: 9 residues within 4Å: Chain A: Y.81, R.84, P.209, G.212, N.312, L.328, Y.331, T.332, M.333 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.328, A:M.333, A:M.333 Water bridges: A:R.84, A:T.332, A:T.332 GOL.5: 4 residues within 4Å: Chain A: I.98, E.144, L.147, E.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.144 GOL.8: 9 residues within 4Å: Chain B: Y.81, R.84, P.209, Q.210, G.212, N.312, L.328, Y.331, M.333 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.84, B:P.209, B:N.312, B:L.328, B:M.333 Water bridges: B:R.84 GOL.9: 7 residues within 4Å: Chain B: R.320, Y.323, E.324, G.325, V.326, E.327 Chain C: R.16 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.320, B:Y.323, B:G.325, B:V.326, B:E.327, C:R.16, C:R.16 Water bridges: B:R.76, B:R.76, B:R.76 GOL.10: 3 residues within 4Å: Chain B: E.258, R.262, E.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.75, B:E.272 GOL.11: 8 residues within 4Å: Chain B: W.237, D.238, P.366, A.367, D.368, F.374, V.375, H.378 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.238, B:D.238, B:A.367, B:D.368, B:V.375, B:V.375 GOL.12: 5 residues within 4Å: Chain B: F.34, I.167, K.387, A.410, I.411 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.387 Water bridges: B:I.167, B:I.167 GOL.13: 5 residues within 4Å: Chain B: K.71, R.75, N.254, I.255, E.258 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.71, B:K.71, B:N.254, B:E.258 Water bridges: B:R.75, B:D.251 GOL.14: 3 residues within 4Å: Chain B: R.321, P.355, S.359 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.321, B:R.321

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: M.111, E.112, R.128, I.189 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.111, A:E.112 Water bridges: A:D.109, A:R.128 Salt bridges: A:R.128 ACT.15: 5 residues within 4Å: Chain B: M.111, E.112, R.128, I.189, R.193 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.189 Hydrogen bonds: B:E.112 Water bridges: B:T.115 Salt bridges: B:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferrer-Orta, C. et al., Dual role of the foot-and-mouth disease virus 3B1 protein in the replication complex: As protein primer and as an essential component to recruit 3Dpol to membranes. Plos Pathog. (2023)

Release Date

2023-04-26

Peptides

RNA-directed RNA polymerase 3D-POL: AB
Protein 3B-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

RNA-directed RNA polymerase 3D-POL

Protein 3B-1

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