MolNFT v1 · #114394 · protein
Structure of a unique ATP synthase subunit neqb from nanoarcheaum equitans
5BO5 · NEQ263: “Structure of a unique ATP synthase subunit neqb from nanoarcheaum equitans”. X-ray diffraction, 2 ligands (MG, SO4), 16 pockets (best druggability 0.71). MolNFT v1 #114394 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5BO5
- Type
- protein
- Length
- 1,557 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NEQ263
- UniProt
- Q74MS5
- Ligands
- MG, SO4
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NEQ263 | protein | 397 | 41% helix, 24% strand | Q74MS5 |
| B | NEQ263 | protein | 392 | 41% helix, 25% strand | Q74MS5 |
| C | NEQ263 | protein | 392 | 40% helix, 24% strand | Q74MS5 |
| D | NEQ263 | protein | 376 | 41% helix, 24% strand | Q74MS5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.71 | 0.83 | 41 | empty |
| 2 | 391 | 0.55 | 0.73 | 47 | empty |
| 3 | 53 | 0.53 | 0.88 | 18 | empty |
| 4 | 174 | 0.49 | 0.77 | 25 | empty |
| 5 | 134 | 0.44 | 0.77 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–C · 646 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 134 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 76 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5BO5 · Structure of a unique ATP synthase subunit NeqB from Nanoarcheaum equitans · the same entry in another collection · chain A against A, TM-score 1.00
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 Q74MS5
- Elsewhere: RCSB PDB 5BO5 · PDBe 5BO5 · UniProt Q74MS5
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