MolNFT v1 · #135947 · protein
Structure of nitrite reductase ania from neisseria gonorrhoeae, space group I4122
5UE6: “Structure of nitrite reductase ania from neisseria gonorrhoeae, space group I4122”. X-ray diffraction, 2 ligands (CU, NA), 20 pockets (best druggability 0.87). MolNFT v1 #135947 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5UE6
- Type
- protein
- Length
- 2,795 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- UniProt
- Q5F7A4
- Ligands
- CU, NA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Nitrite reductase | protein | 314 | 10% helix, 45% strand | Q5F7A4 |
| B, C, E, H | Nitrite reductase | protein | 310 | 9% helix, 45% strand | Q5F7A4 |
| D | Nitrite reductase | protein | 309 | 9% helix, 45% strand | Q5F7A4 |
| F | Nitrite reductase | protein | 307 | 9% helix, 45% strand | Q5F7A4 |
| I | Nitrite reductase | protein | 311 | 10% helix, 45% strand | Q5F7A4 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I
- NA · Sodium ion · metal · 9 copies · chains A, C, B, D, F, E, G, I, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.87 | 0.88 | 118 | CU |
| 2 | 261 | 0.84 | 0.95 | 34 | empty |
| 3 | 250 | 0.83 | 0.95 | 37 | empty |
| 4 | 251 | 0.83 | 0.95 | 35 | empty |
| 5 | 57 | 0.70 | 0.97 | 17 | empty |
Interfaces
13 interfaces between chains.
- H–I · 2259 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2164 Ų buried · 47 hydrogen bonds · protein-protein
- G–H · 2156 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 2150 Ų buried · 47 hydrogen bonds · protein-protein
- D–F · 2140 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 5UE6 · Structure of nitrite reductase AniA from Neisseria gonorrhoeae, space group I4122 · 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 5UE6 · PDBe 5UE6 · UniProt Q5F7A4
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