MolNFT v1 · #16829 · protein
Cytochrome C nitrite reductase from desulfovibrio desulfuricans atcc 27774: the relevance of the two calcium sites in the structure of the catalytic subunit (nrfa).
1OAH: “Cytochrome C nitrite reductase from desulfovibrio desulfuricans atcc 27774: the relevance of the two calcium…”. X-ray diffraction, 4 ligands (HEC, CA, ZN), 10 pockets (best druggability 0.90). MolNFT v1 #16829 on GenesisL1: 3D…
- PDB
- 1OAH
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C nitrite reductase
- EC
- 1.7.2.2
- UniProt
- Q8VNU2
- Ligands
- HEC, CA, ZN, CL
- Pockets
- 10 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C nitrite reductase (EC 1.7.2.2) | protein | 475 | 43% helix, 6% strand | Q8VNU2 |
| B | Cytochrome C nitrite reductase (EC 1.7.2.2) | protein | 482 | 42% helix, 7% strand | Q8VNU2 |
Ligands and binding sites
- HEC · Heme C · ligand · 10 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.90 | 0.92 | 119 | HEC, CA, CL |
| 2 | 652 | 0.89 | 0.93 | 100 | HEC, CA, CL |
| 3 | 587 | 0.76 | 0.82 | 50 | empty |
| 4 | 67 | 0.42 | 0.81 | 20 | empty |
| 5 | 88 | 0.34 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1364 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 cofactor (heme c attachment).
Compared structures
- 1OAH · Cytochrome c Nitrite Reductase from Desulfovibrio desulfuricans ATCC 27774: The relevance… · 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 Q8VNU2
- Elsewhere: RCSB PDB 1OAH · PDBe 1OAH · UniProt Q8VNU2
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