SMTL ID : 1qhd.1

CRYSTAL STRUCTURE OF VP6, THE MAJOR CAPSID PROTEIN OF GROUP A ROTAVIRUS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: H.154 Chain B: H.154 Chain C: H.154 Ligands: CL.2, ZN.8, CL.9, ZN.15, CL.16 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:H.154, C:H.154, B:H.154 ZN.8: 8 residues within 4Å: Chain A: H.154 Chain B: H.154 Chain C: H.154 Ligands: ZN.1, CL.2, CL.9, ZN.15, CL.16 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:H.154, C:H.154, B:H.154 ZN.15: 8 residues within 4Å: Chain A: H.154 Chain B: H.154 Chain C: H.154 Ligands: ZN.1, CL.2, ZN.8, CL.9, CL.16 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:H.154, C:H.154, B:H.154

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

CL.2: 11 residues within 4Å: Chain A: H.154, K.155 Chain B: H.154, K.155 Chain C: H.154, K.155 Ligands: ZN.1, ZN.8, CL.9, ZN.15, CL.16 Ligand excluded by PLIP CL.9: 11 residues within 4Å: Chain A: H.154, K.155 Chain B: H.154, K.155 Chain C: H.154, K.155 Ligands: ZN.1, CL.2, ZN.8, ZN.15, CL.16 Ligand excluded by PLIP CL.16: 11 residues within 4Å: Chain A: H.154, K.155 Chain B: H.154, K.155 Chain C: H.154, K.155 Ligands: ZN.1, CL.2, ZN.8, CL.9, ZN.15 Ligand excluded by PLIP

15 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.3: 2 residues within 4Å: Ligands: CA.10, CA.17 No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: N.267, D.287 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.287, H2O.8 CA.5: 1 residues within 4Å: Chain A: E.380 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.380, H2O.3, H2O.7, H2O.10 CA.6: 1 residues within 4Å: Chain A: Q.48 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: T.152, E.341 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.152, A:E.341, H2O.1, H2O.11 CA.10: 2 residues within 4Å: Ligands: CA.3, CA.17 No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Chain B: N.267, D.287 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.287, H2O.19 CA.12: 1 residues within 4Å: Chain B: E.380 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.380, H2O.14, H2O.18, H2O.21 CA.13: 1 residues within 4Å: Chain B: Q.48 No protein-ligand interaction detected (PLIP) CA.14: 2 residues within 4Å: Chain B: T.152, E.341 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.152, B:E.341, H2O.13, H2O.23 CA.17: 2 residues within 4Å: Ligands: CA.3, CA.10 No protein-ligand interaction detected (PLIP) CA.18: 2 residues within 4Å: Chain C: N.267, D.287 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.287, H2O.30 CA.19: 1 residues within 4Å: Chain C: E.380 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.380, H2O.25, H2O.29, H2O.32 CA.20: 1 residues within 4Å: Chain C: Q.48 No protein-ligand interaction detected (PLIP) CA.21: 2 residues within 4Å: Chain C: T.152, E.341 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.152, C:E.341, H2O.24, H2O.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathieu, M. et al., Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion. EMBO J. (2001)

Release Date

2001-04-13

Peptides

VIRAL CAPSID VP6: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

VIRAL CAPSID VP6

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