MolNFT v1 · #134647 · protein
Structure of nitrite reductase ania from neisseria gonorrhoeae, space group P212121
5TB7: “Structure of nitrite reductase ania from neisseria gonorrhoeae, space group P212121”. X-ray diffraction, 2 ligands (CU, PO4), 12 pockets (best druggability 0.83). MolNFT v1 #134647 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5TB7
- Type
- protein
- Length
- 934 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- UniProt
- Q5F7A4
- Ligands
- CU, PO4
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrite reductase | protein | 312 | 9% helix, 46% strand | Q5F7A4 |
| B, C | Nitrite reductase | protein | 311 | 9% helix, 46% strand | Q5F7A4 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.83 | 0.94 | 36 | empty |
| 2 | 63 | 0.71 | 0.97 | 14 | empty |
| 3 | 59 | 0.46 | 0.84 | 16 | empty |
| 4 | 59 | 0.45 | 0.83 | 16 | empty |
| 5 | 72 | 0.43 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2233 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 2227 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2226 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 5TB7 · Structure of nitrite reductase AniA from Neisseria gonorrhoeae, space group P212121 · 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 Q5F7A4
- Elsewhere: RCSB PDB 5TB7 · PDBe 5TB7 · UniProt Q5F7A4
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