Research workbench
Crystal structure of the pi-bound V1 complex
Analyse Crystal structure of the pi-bound V1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KND
- Type
- protein
- Length
- 3,403 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
- MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 586 | 36% helix, 24% strand | Q08636 |
| B | V-type sodium ATPase catalytic subunit a (EC 3.6.3.15) | protein | 592 | 36% helix, 24% strand | Q08636 |
| D, E | V-type sodium ATPase subunit B | protein | 452 | 37% helix, 23% strand | Q08637 |
| F | V-type sodium ATPase subunit B | protein | 455 | 36% helix, 23% strand | Q08637 |
| G | V-type sodium ATPase subunit D | protein | 178 | 78% helix, 9% strand | P43435 |
| H | V-type sodium ATPase subunit ntpg (F) | protein | 102 | 39% helix, 18% strand | P43455 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
- PO4 · Phosphate ion · ion · chains C, F
- GOL · Glycerol · additive · 3 copies · chains C, F, G
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains F
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 | 673 | 0.88 | 0.93 | 112 | empty |
| 2 | 1055 | 0.86 | 0.87 | 110 | empty |
| 3 | 842 | 0.85 | 0.88 | 87 | empty |
| 4 | 583 | 0.84 | 0.89 | 67 | empty |
| 5 | 1127 | 0.83 | 0.85 | 97 | empty |
Interfaces
15 interfaces between chains.
- C–F · 3261 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2523 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 2463 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2374 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1984 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5KND · Crystal structure of the Pi-bound V1 complex · 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 B 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 0.98
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 5KND · PDBe 5KND · UniProt Q08636 · UniProt Q08637 · UniProt P43435 · UniProt P43455
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