MolNFT v1 · #12621 · protein
Crystal structure of spinach chloroplast F1-ATPase complexed with tentoxin
1KMH · ATPase alpha subunit: “Crystal structure of spinach chloroplast F1-ATPase complexed with tentoxin”. X-ray diffraction, 1 ligand (TTX), 12 pockets (best druggability 0.85). MolNFT v1 #12621 on GenesisL1: 3D structure, binding sites…
- PDB
- 1KMH
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase alpha subunit; ATPase beta subunit
- EC
- 3.6.1.34
- UniProt
- P06450, P00825
- Ligands
- TTX
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATPase alpha subunit (EC 3.6.1.34) | protein | 477 | 35% helix, 16% strand | P06450 |
| B | ATPase beta subunit (EC 3.6.1.34) | protein | 467 | 27% helix, 19% strand | P00825 |
Ligands and binding sites
- TTX · Tentoxin · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.85 | 0.85 | 100 | TTX |
| 2 | 1113 | 0.82 | 0.83 | 115 | empty |
| 3 | 58 | 0.69 | 0.96 | 20 | empty |
| 4 | 138 | 0.55 | 0.82 | 19 | empty |
| 5 | 113 | 0.55 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2024 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1KMH · Crystal Structure of spinach chloroplast F1-ATPase complexed with tentoxin · the same entry in another collection · chain A against A, TM-score 1.00
- P06450 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, chloroplastic (P06450) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P00825 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta, chloroplastic (P00825) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P06450
- Every structure of UniProt P00825
- Elsewhere: RCSB PDB 1KMH · PDBe 1KMH · UniProt P06450 · UniProt P00825
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