Research workbench
Crystal structure of AMP-pnp bound mutant A3B3 complex from enterococcus hirae V-ATPase
Analyse Crystal structure of AMP-pnp bound mutant 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
- 5ZE9
- Type
- protein
- Length
- 3,131 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 0.86
Structure
x-ray diffraction · 6 distinct chains · 37% 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 | 38% helix, 24% strand | Q08636 |
| B | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 592 | 38% helix, 24% strand | Q08636 |
| C | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 587 | 38% helix, 24% strand | Q08636 |
| D | V-type sodium ATPase subunit B | protein | 453 | 37% helix, 25% strand | Q08637 |
| E | V-type sodium ATPase subunit B | protein | 455 | 36% helix, 25% strand | Q08637 |
| F | V-type sodium ATPase subunit B | protein | 456 | 37% helix, 25% strand | Q08637 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 39 copies · chains A, E, D, B, F, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains D
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 | 1063 | 0.86 | 0.87 | 123 | ANP, MG, GOL |
| 2 | 1126 | 0.86 | 0.86 | 128 | ANP, MG, GOL |
| 3 | 947 | 0.85 | 0.86 | 98 | GOL |
| 4 | 654 | 0.84 | 0.88 | 64 | GOL |
| 5 | 579 | 0.84 | 0.89 | 62 | GOL |
Interfaces
6 interfaces between chains.
- C–F · 3191 Ų buried · 49 hydrogen bonds · protein-protein
- B–E · 3114 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 2417 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 1885 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 1852 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5ZE9 · Crystal structure of AMP-PNP bound mutant A3B3 complex from Enterococcus hirae V-ATPase · 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 D against A, 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
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 5ZE9 · PDBe 5ZE9 · UniProt Q08636 · UniProt Q08637
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