MolNFT v1 · #139370 · protein
Crystal structure of human voltage-dependent anion channel 1 (HVDAC1) in C222 space group
5XDO · Voltage-dependent anion-selective channel protein 1: “Crystal structure of human voltage-dependent anion channel 1 (HVDAC1) in C222 space group”. X-ray diffraction, 2 ligands (SPD, LNK), 8 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 5XDO
- Type
- protein
- Length
- 541 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
- SPD, LNK
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Voltage-dependent anion-selective channel protein 1 | protein | 283 | 3% helix, 64% strand | P21796 |
| B | Voltage-dependent anion-selective channel protein 1 | protein | 258 | 3% helix, 62% strand | P21796 |
Ligands and binding sites
- SPD · Spermidine · ligand · 2 copies · chains A, B
- LNK · Pentane · ligand · 2 copies · chains A, B
- OCT · N-octane · additive · 4 copies · chains A, B
- HEX · Hexane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.69 | 0.75 | 56 | OCT |
| 2 | 208 | 0.53 | 0.78 | 37 | SPD |
| 3 | 179 | 0.50 | 0.77 | 32 | SPD |
| 4 | 106 | 0.41 | 0.77 | 23 | empty |
| 5 | 121 | 0.41 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 122 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XDO · Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group · 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 0.98
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 5XDO · PDBe 5XDO · UniProt P21796
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