SMTL ID : 3qid.1 (1 other biounit)

Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: D.407, R.408, H.450 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: T.117, S.118 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: R.405 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: T.25, G.48, S.49, S.58, L.59 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: Y.243, T.244, R.245 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: T.145, H.146, N.149 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: W.131, G.133 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: G.397, D.398, W.402 Chain B: N.234, F.235 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: E.335, N.350, L.351 Ligands: SO4.11 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: S.58, Q.61, R.64 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: R.236, N.350 Ligands: SO4.9 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: K.26, H.423, Q.424, E.428 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: D.407, R.408, H.450 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: T.117, S.118 Ligand excluded by PLIP SO4.19: 1 residues within 4Å: Chain B: R.405 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain B: T.25, G.48, S.49, S.58, L.59 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: Y.243, T.244, R.245 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: T.145, H.146, N.149 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: W.131, G.133 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain A: N.234, F.235 Chain B: G.397, D.398, W.402 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: E.335, N.350, L.351 Ligands: SO4.27 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: S.58, Q.61, R.64 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: R.236, N.350 Ligands: SO4.25 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: K.26, H.423, Q.424, E.428 Ligand excluded by PLIP

2 x MN3: MANGANESE (III) ION(Non-covalent)

MN3.13: 2 residues within 4Å: Chain A: D.240, D.344 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.344, H2O.4, H2O.5, H2O.5, H2O.5 MN3.29: 2 residues within 4Å: Chain B: D.240, D.344 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.344, H2O.10, H2O.12, H2O.12, H2O.12

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain A: P.79, Q.80, E.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.80, A:E.81 GOL.15: 4 residues within 4Å: Chain A: S.220, M.221, N.222, D.491 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.221, A:N.222, A:N.222 GOL.16: 3 residues within 4Å: Chain A: G.154, K.155, S.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 GOL.30: 3 residues within 4Å: Chain B: P.79, Q.80, E.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.80, B:E.81 GOL.31: 4 residues within 4Å: Chain B: S.220, M.221, N.222, D.491 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.221, B:N.222, B:N.222 GOL.32: 3 residues within 4Å: Chain B: G.154, K.155, S.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J.H. et al., Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase. J.Gen.Virol. (2011)

Release Date

2011-12-21

Peptides

RNA dependent RNA polymerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

RNA dependent RNA polymerase

Related Entries With Identical Sequence