MolNFT v1 · #139369 · protein
Crystal structure of human voltage-dependent anion channel 1 (HVDAC1) in P22121 space group
5XDN · Voltage-dependent anion-selective channel protein 1: “Crystal structure of human voltage-dependent anion channel 1 (HVDAC1) in P22121 space group”. X-ray diffraction, 2 ligands (D12, D10), 11 pockets (best druggability 0.73). MolNFT…
- PDB
- 5XDN
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Voltage-dependent anion-selective channel protein 1
- UniProt
- P21796
- Ligands
- D12, D10
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Voltage-dependent anion-selective channel protein 1 | protein | 278 | 3% helix, 65% strand | P21796 |
| B | Voltage-dependent anion-selective channel protein 1 | protein | 271 | 3% helix, 64% strand | P21796 |
Ligands and binding sites
- D12 · Dodecane · ligand · 2 copies · chains A, B
- D10 · Decane · ligand · 2 copies · chains A, B
- HEX · Hexane · additive · 4 copies · chains A, B
- OCT · N-octane · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.73 | 0.78 | 53 | OCT, D10, D12, HEX |
| 2 | 180 | 0.49 | 0.77 | 29 | empty |
| 3 | 161 | 0.46 | 0.76 | 26 | empty |
| 4 | 117 | 0.43 | 0.77 | 21 | empty |
| 5 | 65 | 0.41 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 591 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XDN · Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space… · the same entry in another collection · chain A against A, TM-score 1.00
- P21796 · AlphaFold monomer V2.0 prediction for voltage-dependent anion- selective channel protein… · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21796
- Elsewhere: RCSB PDB 5XDN · PDBe 5XDN · UniProt P21796
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