Research workbench
Crystal structure of enterococcus hirae V1-ATPase [EV1]
Analyse Crystal structure of enterococcus hirae V1-ATPase [EV1] in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VR4
- Type
- protein
- Length
- 3,409 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
- Ligands
- CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 23% 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, 24% strand | Q08636 |
| B | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 593 | 37% helix, 24% strand | Q08636 |
| C | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 586 | 36% helix, 24% 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 | 455 | 36% helix, 25% strand | Q08637 |
| G | V-type sodium ATPase subunit D (EC 3.6.3.15) | protein | 181 | 80% helix, 9% strand | — |
| H | V-type sodium ATPase subunit G (EC 3.6.3.15) | protein | 102 | 45% helix, 21% strand | P43455 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B, E
- GOL · Glycerol · additive · 8 copies · chains A, B, D, C, F, G
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 900 | 0.89 | 0.91 | 135 | empty |
| 2 | 1086 | 0.86 | 0.87 | 115 | empty |
| 3 | 1029 | 0.85 | 0.86 | 94 | empty |
| 4 | 265 | 0.84 | 0.95 | 43 | empty |
| 5 | 526 | 0.84 | 0.90 | 55 | empty |
Interfaces
15 interfaces between chains.
- C–F · 3275 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 2536 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 2458 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2271 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2076 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 122 modified (engineered).
Compared structures
- 3VR4 · Crystal structure of Enterococcus hirae V1-ATPase [eV1] · the same entry in another collection · chain H against H, 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 0.99
- 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 3VR4 · PDBe 3VR4 · UniProt Q08636 · UniProt Q08637 · UniProt P43455
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