SMTL ID : 5xdo.1

Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x SPD: SPERMIDINE(Non-covalent)

SPD.1: 5 residues within 4Å: Chain A: Y.19, L.22, Q.166, H.193, N.195 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.22, A:N.195 Hydrogen bonds: A:Q.166 SPD.7: 6 residues within 4Å: Chain B: Y.19, L.22, R.27, H.193, T.194, N.195 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.19, B:L.22, B:N.195 Hydrogen bonds: B:L.22, B:R.27, B:T.194

4 x OCT: N-OCTANE(Non-covalent)

OCT.2: 6 residues within 4Å: Chain A: L.220, N.226, T.229 Chain B: T.229, F.231 Ligands: OCT.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.229, B:F.231, A:L.220 OCT.3: 2 residues within 4Å: Chain A: S.179, F.181 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.181, A:F.181 OCT.8: 5 residues within 4Å: Chain A: L.220, T.229, F.231 Chain B: L.220 Ligands: OCT.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.231, A:F.231 OCT.9: 4 residues within 4Å: Chain A: F.231 Chain B: F.202, W.222, G.225 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.202, B:F.202, B:W.222, A:F.231, A:F.231

2 x LNK: PENTANE(Non-covalent)

LNK.4: 2 residues within 4Å: Chain A: Y.165, F.181 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.165, A:F.181 LNK.5: 1 residues within 4Å: Chain B: F.190 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.190

1 x HEX: HEXANE(Non-covalent)

HEX.6: 2 residues within 4Å: Chain A: R.132, L.137 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hosaka, T. et al., Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1. Protein Sci. (2017)

Release Date

2017-06-28

Peptides

Voltage-dependent anion-selective channel protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent anion-selective channel protein 1

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