SMTL ID : 3ur0.4 (3 other biounits)

Crystal structures of murine norovirus RNA-dependent RNA polymerase in complex with Suramin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-hexamer

Ligands

6 x SVR: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC ACID(Non-covalent)

SVR.1: 10 residues within 4Å: Chain A: P.38, P.39, G.40, A.41, W.42, K.171, A.409, D.412, R.413, L.416 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.41 Hydrogen bonds: A:W.42, A:W.42 Salt bridges: A:K.171 SVR.2: 14 residues within 4Å: Chain A: W.42, D.65, Q.66, K.68, E.168, V.170, K.171, K.174, K.180, K.181, R.182, R.245, R.392 Ligands: SO4.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.68, A:V.170, A:K.174, A:K.180, A:R.182, A:R.245 Hydrogen bonds: A:Q.66, A:K.68, A:K.171, A:R.245 Salt bridges: A:K.171, A:K.174 pi-Stacking: A:W.42 pi-Cation interactions: A:K.180 SVR.6: 10 residues within 4Å: Chain B: P.38, P.39, G.40, A.41, W.42, K.171, A.409, D.412, R.413, L.416 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.41 Hydrogen bonds: B:W.42, B:W.42 Salt bridges: B:K.171 SVR.7: 14 residues within 4Å: Chain B: W.42, D.65, Q.66, K.68, E.168, V.170, K.171, K.174, K.180, K.181, R.182, R.245, R.392 Ligands: SO4.10 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.68, B:V.170, B:K.174, B:K.180, B:R.182, B:R.245 Hydrogen bonds: B:Q.66, B:K.68, B:K.171, B:R.245 Salt bridges: B:K.171, B:K.174 pi-Stacking: B:W.42 pi-Cation interactions: B:K.180 SVR.14: 8 residues within 4Å: Chain D: P.38, P.39, G.40, A.41, W.42, A.409, D.412, R.413 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.41 Hydrogen bonds: D:P.38, D:W.42, D:W.42 Salt bridges: D:R.413 SVR.19: 8 residues within 4Å: Chain F: P.38, P.39, G.40, A.41, W.42, A.409, D.412, R.413 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:A.41 Hydrogen bonds: F:P.38, F:W.42, F:W.42 Salt bridges: F:R.413

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

SO4.3: 5 residues within 4Å: Chain A: T.25, G.48, S.49, S.58, L.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.49, A:L.59 SO4.4: 4 residues within 4Å: Chain A: T.8, Y.9, A.10, R.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.8, A:A.10 SO4.5: 4 residues within 4Å: Chain A: Y.243, T.244, R.245 Ligands: SVR.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.245 SO4.8: 5 residues within 4Å: Chain B: T.25, G.48, S.49, S.58, L.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.49, B:L.59 SO4.9: 4 residues within 4Å: Chain B: T.8, Y.9, A.10, R.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.8, B:A.10 SO4.10: 4 residues within 4Å: Chain B: Y.243, T.244, R.245 Ligands: SVR.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.245 SO4.11: 2 residues within 4Å: Chain C: W.42 Ligands: SO4.12 No protein-ligand interaction detected (PLIP) SO4.12: 5 residues within 4Å: Chain C: W.42, V.170, K.171, K.174 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.171 Salt bridges: C:K.171, C:K.174 SO4.13: 6 residues within 4Å: Chain C: G.40, A.41, W.42, A.409, D.412, R.413 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.40, C:W.42, C:A.409 Salt bridges: C:R.413 SO4.15: 4 residues within 4Å: Chain D: W.42, V.170, K.171, K.174 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.171 Water bridges: D:K.174 Salt bridges: D:K.174 SO4.16: 2 residues within 4Å: Chain E: W.42 Ligands: SO4.17 No protein-ligand interaction detected (PLIP) SO4.17: 5 residues within 4Å: Chain E: W.42, V.170, K.171, K.174 Ligands: SO4.16 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.171 Water bridges: E:E.168 Salt bridges: E:K.171, E:K.174 SO4.18: 6 residues within 4Å: Chain E: G.40, A.41, W.42, A.409, D.412, R.413 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.40, E:W.42, E:A.409 Salt bridges: E:R.413 SO4.20: 4 residues within 4Å: Chain F: W.42, V.170, K.171, K.174 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.171 Water bridges: F:K.174 Salt bridges: F:K.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mastrangelo, E. et al., Structure-Based Inhibition of Norovirus RNA-Dependent RNA Polymerases. J.Mol.Biol. (2012)

Release Date

2012-05-02

Peptides

RNA-dependent RNA polymerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
A

D
B

E
A

F
B

RNA-dependent RNA polymerase

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