MolNFT v1 · #34919 · protein
Crystal structure of nitrite reductase from hyphomicrobium denitrificans
2DV6: “Crystal structure of nitrite reductase from hyphomicrobium denitrificans”. X-ray diffraction, 2 ligands (CU, K), 15 pockets (best druggability 0.83). MolNFT v1 #34919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DV6
- Type
- protein
- Length
- 2,532 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.2.1
- UniProt
- Q8KKH4
- Ligands
- CU, K
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nitrite reductase (EC 1.7.2.1) | protein | 422 | 9% helix, 46% strand | Q8KKH4 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 18 copies · chains A, C, B, D, F, E
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.83 | 0.88 | 83 | empty |
| 2 | 933 | 0.82 | 0.84 | 81 | empty |
| 3 | 963 | 0.82 | 0.83 | 86 | empty |
| 4 | 1099 | 0.81 | 0.82 | 93 | empty |
| 5 | 1079 | 0.81 | 0.82 | 95 | empty |
Interfaces
9 interfaces between chains.
- D–E · 2421 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2397 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2396 Ų buried · 38 hydrogen bonds · protein-protein
- D–F · 2392 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2390 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2DV6 · Crystal structure of nitrite reductase from Hyphomicrobium denitrificans · the same entry in another collection · chain B against B, 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 Q8KKH4
- Elsewhere: RCSB PDB 2DV6 · PDBe 2DV6 · UniProt Q8KKH4
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