SMTL ID : 3ddk.1

Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

9 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: E.4, N.65, R.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.4, A:N.65, A:N.67, A:R.284 Water bridges: A:N.65 NA.2: 2 residues within 4Å: Chain A: K.38, D.397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.397, A:D.397 NA.3: 5 residues within 4Å: Chain A: R.188, Y.195, S.292, G.293 Ligands: SO4.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.188, A:S.292, A:G.293 NA.4: 4 residues within 4Å: Chain A: L.229, E.366, V.367 Ligands: SO4.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.229, A:E.366, A:V.367 NA.5: 3 residues within 4Å: Chain A: H.69, D.71, E.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.69, A:E.72 NA.6: 2 residues within 4Å: Chain A: H.199, V.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.199 NA.7: 3 residues within 4Å: Chain A: F.34, E.35, H.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.35, A:K.436 NA.8: 1 residues within 4Å: Chain A: Y.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.385 NA.9: 2 residues within 4Å: Chain A: Y.314, K.315 No protein-ligand interaction detected (PLIP)

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

SO4.10: 5 residues within 4Å: Chain A: K.38, L.162, R.163, R.174, K.376 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.162 Water bridges: A:K.376 Salt bridges: A:K.38, A:R.163, A:R.174, A:K.376 SO4.11: 4 residues within 4Å: Chain A: R.174, Y.234, S.235, G.236 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.236 Water bridges: A:K.167, A:K.167, A:Y.237, A:Y.237 Salt bridges: A:R.174 SO4.12: 3 residues within 4Å: Chain A: R.44, S.45, R.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.45, A:S.45 Water bridges: A:G.46 Salt bridges: A:R.277 SO4.13: 4 residues within 4Å: Chain A: P.243, A.247, D.267, C.270 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.271 Salt bridges: A:K.250 SO4.14: 4 residues within 4Å: Chain A: L.110, D.111, R.188 Ligands: NA.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.111 Water bridges: A:T.114, A:S.184, A:S.184 Salt bridges: A:K.127, A:R.188 SO4.15: 8 residues within 4Å: Chain A: G.227, H.228, L.229, E.366, V.367, T.368, W.369 Ligands: NA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.229, A:V.367, A:W.369 Salt bridges: A:H.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campagnola, G. et al., Crystal Structure of Coxsackievirus B3 3Dpol Highlights Functional Importance of Residue 5 in Picornaviral Polymerases. J.Virol. (2008)

Release Date

2008-09-23

Peptides

RNA polymerase B3 3Dpol: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA polymerase B3 3Dpol

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