MolNFT v1 · #114358 · protein
Structure of a unique ATP synthase neqa-neqb in complex with anp from nanoarcheaum equitans
5BN4 · V-type ATP synthase alpha chain: “Structure of a unique ATP synthase neqa-neqb in complex with anp from nanoarcheaum equitans”. X-ray diffraction, 2 ligands (ANP, MG), 14 pockets (best druggability 0.86). MolNFT v1 #114358 on…
- PDB
- 5BN4
- Type
- protein
- Length
- 980 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase alpha chain; NEQ263
- EC
- 3.6.3.14
- UniProt
- Q74MJ7, Q74MS5
- Ligands
- ANP, MG
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 567 | 35% helix, 23% strand | Q74MJ7 |
| B | NEQ263 | protein | 413 | 36% helix, 22% strand | Q74MS5 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.86 | 0.91 | 56 | empty |
| 2 | 1089 | 0.84 | 0.85 | 91 | ANP |
| 3 | 216 | 0.65 | 0.84 | 30 | empty |
| 4 | 85 | 0.58 | 0.87 | 15 | empty |
| 5 | 167 | 0.57 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2788 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5BN4 · Structure of a unique ATP synthase NeqA-NeqB in complex with ANP from Nanoarcheaum… · the same entry in another collection · chain A against A, TM-score 1.00
- Q74MJ7 · AlphaFold monomer V2.0 prediction for V-type ATP synthase alpha chain (Q74MJ7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q74MJ7
- Every structure of UniProt Q74MS5
- Elsewhere: RCSB PDB 5BN4 · PDBe 5BN4 · UniProt Q74MJ7 · UniProt Q74MS5
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