Research workbench
Crystal structure of AMP-pnp bound A3B3 complex from enterococcus hirae V-ATPase [BA3B3]
Analyse Crystal structure of AMP-pnp bound A3B3 complex from enterococcus hirae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VR3
- Type
- protein
- Length
- 3,105 residues
- Chains
- 6
- 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
- EC
- 3.6.3.15
- UniProt
- Q08636, Q08637
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 34% 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 | 586 | 35% helix, 24% strand | Q08636 |
| B | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 586 | 33% helix, 23% strand | Q08636 |
| C | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 584 | 34% helix, 25% strand | Q08636 |
| D | V-type sodium ATPase subunit B (EC 3.6.3.15) | protein | 447 | 34% helix, 23% strand | Q08637 |
| E, F | V-type sodium ATPase subunit B (EC 3.6.3.15) | protein | 451 | 36% helix, 25% strand | Q08637 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, E, C, F
- MG · Magnesium ion · metal · 2 copies · chains B, E, 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 | 987 | 0.85 | 0.86 | 104 | empty |
| 2 | 607 | 0.85 | 0.90 | 59 | empty |
| 3 | 340 | 0.84 | 0.94 | 43 | empty |
| 4 | 1070 | 0.83 | 0.84 | 118 | empty |
| 5 | 975 | 0.81 | 0.82 | 94 | empty |
Interfaces
6 interfaces between chains.
- C–F · 2728 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 2597 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2535 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1785 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1501 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 111 modified (engineered).
Compared structures
- 3VR3 · Crystal structure of AMP-PNP bound A3B3 complex from Enterococcus hirae V-ATPase [bA3B3] · the same entry in another collection · chain F against F, TM-score 1.00
- Q08637 · AlphaFold monomer V2.0 prediction for V-type sodium ATPase subunit B (Q08637) · a predicted model of the same protein · chain E against A, TM-score 0.99
- 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
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
- Elsewhere: RCSB PDB 3VR3 · PDBe 3VR3 · UniProt Q08636 · UniProt Q08637
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