MolNFT v1 · #106043 · protein
Crystal structure of the subunit df-assembly of the eukaryotic V- ATPase.
4RND · V-type proton ATPase subunit D: “Crystal structure of the subunit df-assembly of the eukaryotic V- ATPase.”. X-ray diffraction, 4 pockets (best druggability 0.46). MolNFT v1 #106043 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4RND
- Type
- protein
- Length
- 578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase subunit D; V-type proton ATPase subunit F
- UniProt
- P32610, P39111
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type proton ATPase subunit D | protein | 178 | 72% helix, 11% strand | P32610 |
| B | V-type proton ATPase subunit F | protein | 118 | 40% helix, 19% strand | P39111 |
| C | V-type proton ATPase subunit D | protein | 167 | 69% helix, 12% strand | P32610 |
| D | V-type proton ATPase subunit F | protein | 115 | 40% helix, 23% strand | P39111 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.46 | 0.80 | 20 | empty |
| 2 | 104 | 0.45 | 0.79 | 21 | empty |
| 3 | 54 | 0.43 | 0.83 | 12 | empty |
| 4 | 81 | 0.43 | 0.80 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–C · 3237 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2185 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2059 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4RND · Crystal Structure of the subunit DF-assembly of the eukaryotic V-ATPase. · the same entry in another collection · chain D against D, TM-score 1.00
- P39111 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit F (P39111) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P32610 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit D (P32610) · a predicted model of the same protein · chain C against A, TM-score 0.72
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 P32610
- Every structure of UniProt P39111
- Elsewhere: RCSB PDB 4RND · PDBe 4RND · UniProt P32610 · UniProt P39111
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