MolNFT v1 · #15661 · protein
The structure of bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan
1NBM: “The structure of bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan”. X-ray diffraction, 4 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #15661 on GenesisL1: 3D structure, binding sites…
- PDB
- 1NBM
- Type
- protein
- Length
- 2,987 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F1-ATPase
- EC
- 3.6.1.34
- UniProt
- P19483, P00829, P05631
- Ligands
- ATP, ADP, MG, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | F1-ATPase (EC 3.6.1.34) | protein | 487 | 43% helix, 21% strand | P19483 |
| C | F1-ATPase (EC 3.6.1.34) | protein | 492 | 41% helix, 21% strand | P19483 |
| D | F1-ATPase (EC 3.6.1.34) | protein | 467 | 36% helix, 21% strand | P00829 |
| E | F1-ATPase (EC 3.6.1.34) | protein | 466 | 41% helix, 20% strand | P00829 |
| F | F1-ATPase (EC 3.6.1.34) | protein | 466 | 37% helix, 20% strand | P00829 |
| G | F1-ATPase (EC 3.6.1.34) | protein | 122 | 88% helix, 0% strand | P05631 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · chains C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- PO4 · Phosphate ion · ion · chains 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 | 898 | 0.89 | 0.91 | 101 | MG, ATP |
| 2 | 718 | 0.87 | 0.91 | 90 | MG, ATP |
| 3 | 729 | 0.85 | 0.88 | 87 | MG, ADP |
| 4 | 522 | 0.83 | 0.89 | 67 | empty |
| 5 | 995 | 0.83 | 0.84 | 78 | MG, ATP |
Interfaces
13 interfaces between chains.
- C–D · 2700 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2600 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 2352 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 2188 Ų buried · 35 hydrogen bonds · protein-protein
- B–E · 1943 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 1NBM · The structure of bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan · the same entry in another collection · chain G against G, TM-score 1.00
- P19483 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, mitochondrial (P19483) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P00829 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta, mitochondrial (P00829) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P05631 · AlphaFold monomer V2.0 prediction for ATP synthase subunit gamma, mitochondrial (P05631) · a predicted model of the same protein · chain G against A, TM-score 0.94
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 P19483
- Every structure of UniProt P00829
- Every structure of UniProt P05631
- Elsewhere: RCSB PDB 1NBM · PDBe 1NBM · UniProt P19483 · UniProt P00829 · UniProt P05631
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