MolNFT v1 · #124716 · protein
Crystal structure of the pi-bound V1 complex
5KND: “Crystal structure of the pi-bound V1 complex”. X-ray diffraction, 2 ligands (MG, PO4). MolNFT v1 #124716 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KND
- Type
- protein
- Length
- 3,403 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q08636, Q08637, P43435, P43455
- Ligands
- MG, PO4
Structure
x-ray diffraction · 6 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | — | protein | 586 | — | Q08636 |
| B | — | protein | 592 | — | Q08636 |
| D, E | — | protein | 452 | — | Q08637 |
| F | — | protein | 455 | — | Q08637 |
| G | — | protein | 178 | — | P43435 |
| H | — | protein | 102 | — | 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.
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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