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Structure of a unique ATP synthase neqa-neqb in complex with ADP from nanoarcheaum equitans
Analyse Structure of a unique ATP synthase neqa-neqb in complex with ADP from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BN3
- Type
- protein
- Length
- 970 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
- ADP, MG, SO4
- Pockets
- 11 · best druggability 0.84
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 | 563 | 34% helix, 23% strand | Q74MJ7 |
| B | NEQ263 | protein | 407 | 38% helix, 23% strand | Q74MS5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- DIO · 1,4-diethylene dioxide · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.84 | 0.86 | 93 | GOL, MG |
| 2 | 637 | 0.81 | 0.86 | 58 | ADP, MG, GOL |
| 3 | 669 | 0.71 | 0.78 | 52 | DIO |
| 4 | 184 | 0.57 | 0.81 | 21 | GOL |
| 5 | 171 | 0.56 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2916 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5BN3 · Structure of a unique ATP synthase NeqA-NeqB in complex with ADP 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 5BN3 · PDBe 5BN3 · UniProt Q74MJ7 · UniProt Q74MS5
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