Research workbench
Crystal structure of nucleotide-free enterococcus hirae V1-ATPase [EV1(L)]
Analyse Crystal structure of nucleotide-free enterococcus hirae V1-ATPase [EV1(L)] in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VR5
- Type
- protein
- Length
- 3,354 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type sodium ATPase catalytic subunit a; V-type sodium ATPase subunit B; V-type sodium…
- EC
- 3.6.3.15
- UniProt
- Q08636, Q08637, P43455
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 588 | 36% helix, 25% strand | Q08636 |
| B | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 593 | 37% helix, 25% strand | Q08636 |
| C | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 563 | 34% helix, 26% strand | Q08636 |
| D, E | V-type sodium ATPase subunit B (EC 3.6.3.15) | protein | 452 | 37% helix, 23% strand | Q08637 |
| F | V-type sodium ATPase subunit B (EC 3.6.3.15) | protein | 448 | 36% helix, 25% strand | Q08637 |
| G | V-type sodium ATPase subunit D (EC 3.6.3.15) | protein | 164 | 82% helix, 6% strand | — |
| H | V-type sodium ATPase subunit G (EC 3.6.3.15) | protein | 94 | 50% helix, 23% strand | P43455 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.88 | 0.89 | 145 | empty |
| 2 | 594 | 0.86 | 0.91 | 100 | empty |
| 3 | 1028 | 0.85 | 0.86 | 100 | empty |
| 4 | 1059 | 0.84 | 0.85 | 90 | empty |
| 5 | 740 | 0.84 | 0.87 | 79 | empty |
Interfaces
14 interfaces between chains.
- B–E · 2326 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2311 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 2177 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1712 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1320 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 122 modified (engineered).
Compared structures
- 3VR5 · Crystal structure of nucleotide-free Enterococcus hirae V1-ATPase [eV1(L)] · the same entry in another collection · chain E against E, TM-score 1.00
- Q08636 · AlphaFold monomer V2.0 prediction for V-type sodium ATPase catalytic subunit a (Q08636) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q08637 · AlphaFold monomer V2.0 prediction for V-type sodium ATPase subunit B (Q08637) · a predicted model of the same protein · chain D 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 Q08636
- Every structure of UniProt Q08637
- Every structure of UniProt P43455
- Elsewhere: RCSB PDB 3VR5 · PDBe 3VR5 · UniProt Q08636 · UniProt Q08637 · UniProt P43455
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