SMTL ID : 5xdn.1

Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-dimer

Ligands

2 x D12: DODECANE(Non-covalent)

D12.1: 7 residues within 4Å: Chain A: Y.158 Chain B: F.231, V.249, N.250, S.253, I.255, G.277 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.231, B:V.249, B:I.255, A:Y.158, A:Y.158, A:Y.158 D12.6: 6 residues within 4Å: Chain A: A.104, R.105, Y.130, L.137 Chain B: F.202, W.222 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.105, A:Y.130, A:Y.130, A:L.137, B:F.202, B:F.202

4 x HEX: HEXANE(Non-covalent)

HEX.2: 2 residues within 4Å: Chain A: M.141 Ligands: D10.4 No protein-ligand interaction detected (PLIP) HEX.7: 3 residues within 4Å: Chain B: E.85, L.93, T.95 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.93 HEX.8: 1 residues within 4Å: Chain B: F.181 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.181, B:F.181 HEX.9: 4 residues within 4Å: Chain A: A.163, F.181 Chain B: T.216, V.218 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.216, B:V.218, A:F.181

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

OCT.3: 6 residues within 4Å: Chain A: I.150, M.167, F.169 Chain B: F.190, L.192 Ligands: D10.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.150, A:F.169, A:F.169, B:F.190, B:L.192

2 x D10: DECANE(Non-covalent)

D10.4: 6 residues within 4Å: Chain A: C.139, I.150 Chain B: W.161, Y.185 Ligands: HEX.2, OCT.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.150, B:W.161, B:Y.185 D10.5: 2 residues within 4Å: Chain B: A.104, Y.130 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.104, B:Y.130, B:Y.130

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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