SMTL ID : 3j9s.1 (2 other biounits)

Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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.5, CL.6, ZN.9, CL.10 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:H.154, A:H.154, B:H.154 ZN.5: 8 residues within 4Å: Chain A: H.154 Chain B: H.154 Chain C: H.154 Ligands: ZN.1, CL.2, CL.6, ZN.9, CL.10 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:H.154, A:H.154, B:H.154 ZN.9: 8 residues within 4Å: Chain A: H.154 Chain B: H.154 Chain C: H.154 Ligands: ZN.1, CL.2, ZN.5, CL.6, CL.10 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:H.154, A:H.154, B:H.154

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

CL.2: 9 residues within 4Å: Chain A: K.155 Chain B: H.154, K.155 Chain C: K.155 Ligands: ZN.1, ZN.5, CL.6, ZN.9, CL.10 Ligand excluded by PLIP CL.6: 9 residues within 4Å: Chain A: K.155 Chain B: K.155 Chain C: H.154, K.155 Ligands: ZN.1, CL.2, ZN.5, ZN.9, CL.10 Ligand excluded by PLIP CL.10: 9 residues within 4Å: Chain A: H.154, K.155 Chain B: K.155 Chain C: K.155 Ligands: ZN.1, CL.2, ZN.5, CL.6, ZN.9 Ligand excluded by PLIP

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

CA.3: 2 residues within 4Å: Ligands: CA.7, CA.11 No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: V.218, D.287 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Ligands: CA.3, CA.11 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain B: V.218, D.287 No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Ligands: CA.3, CA.7 No protein-ligand interaction detected (PLIP) CA.12: 2 residues within 4Å: Chain C: V.218, D.287 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grant, T. et al., Measuring the optimal exposure for single particle cryo-EM using a 2.6 angstrom reconstruction of rotavirus VP6. Elife (2015)

Release Date

2015-03-11

Peptides

Intermediate capsid protein VP6: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Intermediate capsid protein VP6

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