MolNFT v1 · #124714 · protein
Crystal structure of the 2 ADP-bound V1 complex
5KNB · V-type sodium ATPase catalytic subunit a: “Crystal structure of the 2 ADP-bound V1 complex”. X-ray diffraction, 2 ligands (ADP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #124714 on GenesisL1: 3D structure, binding sites…
- PDB
- 5KNB
- Type
- protein
- Length
- 3,386 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, P43435, P43455
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 8 distinct chains · 37% 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 | 587 | 32% helix, 25% strand | Q08636 |
| B | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 592 | 36% helix, 24% strand | Q08636 |
| C | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 586 | 34% helix, 22% strand | Q08636 |
| D | V-type sodium ATPase subunit B | protein | 453 | 32% helix, 22% strand | Q08637 |
| E | V-type sodium ATPase subunit B | protein | 454 | 37% helix, 24% strand | Q08637 |
| F | V-type sodium ATPase subunit B | protein | 455 | 36% helix, 24% strand | Q08637 |
| G | V-type sodium ATPase subunit D | protein | 164 | 78% helix, 9% strand | P43435 |
| H | V-type sodium ATPase subunit ntpg (F) | protein | 95 | 43% helix, 19% strand | P43455 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, E, C, F
- MG · Magnesium ion · metal · 2 copies · chains B, C
- GOL · Glycerol · additive · 2 copies · chains B, E
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 | 1069 | 0.89 | 0.91 | 150 | empty |
| 2 | 377 | 0.84 | 0.93 | 45 | empty |
| 3 | 636 | 0.82 | 0.87 | 65 | MG, ADP |
| 4 | 292 | 0.82 | 0.93 | 66 | empty |
| 5 | 571 | 0.81 | 0.87 | 80 | empty |
Interfaces
13 interfaces between chains.
- C–F · 3253 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 2418 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2294 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2251 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 1806 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5KNB · Crystal structure of the 2 ADP-bound V1 complex · the same entry in another collection · chain H against H, 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
- Every structure of UniProt P43435
- Every structure of UniProt P43455
- Elsewhere: RCSB PDB 5KNB · PDBe 5KNB · UniProt Q08636 · UniProt Q08637 · UniProt P43435 · UniProt P43455
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