SMTL ID : 3cdu.1

Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex with a pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: Y.314, K.315, G.316 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: K.220, H.466, H.468 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: F.34, E.35, H.399, K.436 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: P.202, C.212, D.213, F.217 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.159, D.160 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.163, R.174 Ligands: GOL.34 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 5 residues within 4Å: Chain A: Y.385, F.387, L.388, L.459, H.463 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.463

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

ACT.8: 3 residues within 4Å: Chain A: P.20, S.21, K.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.22 Hydrogen bonds: A:S.21, A:S.21, A:K.22 ACT.9: 3 residues within 4Å: Chain A: K.22, R.44 Ligands: GOL.43 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.22 Salt bridges: A:K.22, A:R.44 ACT.10: 6 residues within 4Å: Chain A: N.425, G.426, E.427, H.428, E.429 Ligands: GOL.39 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.429 Hydrogen bonds: A:E.429 ACT.11: 3 residues within 4Å: Chain A: S.132, K.133, K.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.133, A:K.134 Salt bridges: A:K.134 ACT.12: 6 residues within 4Å: Chain A: T.68, P.243, V.244, A.247 Ligands: ACT.13, GOL.28 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.243 Water bridges: A:T.68 ACT.13: 3 residues within 4Å: Chain A: H.69, V.70 Ligands: ACT.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.70 Hydrogen bonds: A:V.70

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.14: 10 residues within 4Å: Chain A: K.38, E.161, L.162, R.163, S.164, K.167, R.174, K.376 Ligands: GOL.17, GOL.24 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.164, A:R.174 Salt bridges: A:K.38, A:K.38, A:R.163, A:R.163, A:R.174, A:K.376

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 6 residues within 4Å: Chain A: H.199, V.210, S.295, Y.327 Ligands: GOL.16, GOL.36 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: G.290, C.291, G.293, T.294, S.295 Ligands: GOL.15, GOL.36 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain A: K.38, L.162, D.397, E.400, S.401 Ligands: POP.14 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: Q.384, Y.385, R.455, L.459 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: A.450, S.452, T.453, R.456 Ligands: GOL.20 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain A: T.453, R.456, K.457 Ligands: GOL.19 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: R.416, L.448, P.449, A.450, T.453, K.457 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain A: Y.378, R.380, V.392, P.394 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain A: P.222, W.369, F.379, V.389 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain A: S.164, E.166, K.167, K.360 Ligands: POP.14 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain A: G.211, C.212, P.214, Y.327, L.375, R.377 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain A: M.393, D.397, S.401, L.418, L.421 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain A: L.150, N.151, K.261, N.264, Y.265 Ligand excluded by PLIP GOL.28: 9 residues within 4Å: Chain A: P.243, F.246, A.247, K.250, I.266, D.267, C.270, N.271 Ligands: ACT.12 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain A: I.3, I.6, E.55, F.59, K.279, Y.281 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain A: L.43, R.44, S.45, F.54, E.55, Y.276, R.277 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain A: R.380, H.390, V.392, H.424, N.425, G.426 Ligands: GOL.38 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain A: I.58, K.61, S.173, R.174, L.175 Ligands: GOL.33, GOL.34 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain A: I.58, F.59, S.60, K.61, Y.62, A.239 Ligands: GOL.32 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain A: K.61, R.174, Y.234, S.235, G.236 Ligands: CL.6, GOL.32 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain A: G.316, I.317, D.318, Y.335, W.337 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain A: L.107, R.188, Y.195, H.199, S.292, G.293 Ligands: GOL.15, GOL.16 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain A: H.31, G.36, R.403, W.404 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain A: A.381, D.382, E.383, H.390 Ligands: GOL.31, GOL.39 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain A: G.426, E.427, H.428, F.451 Ligands: ACT.10, GOL.38 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain A: P.338, I.339, D.340 Ligand excluded by PLIP GOL.41: 3 residues within 4Å: Chain A: D.129, K.140, K.147 Ligand excluded by PLIP GOL.42: 3 residues within 4Å: Chain A: T.114, S.115, A.178 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain A: D.47, P.48, R.49 Ligands: ACT.9, GOL.44 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain A: E.39, P.40, R.49, W.404 Ligands: GOL.43 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gruez, A. et al., The crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on Picornaviridae polymerases. J.Virol. (2008)

Release Date

2008-07-22

Peptides

RNA-directed RNA polymerase 3D-POL: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-directed RNA polymerase 3D-POL

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