Research workbench
Crystal structure of cytochrome C nitrite reductase nrfha complex bound to the hqno inhibitor
Analyse Crystal structure of cytochrome C nitrite reductase nrfha complex bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VR0
- Type
- protein
- Length
- 2,272 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C nitrite reductase, catalytic subunit nfra; NAPC/NIRT cytochrome C family…
- EC
- 1.7.2.2, 1.10.2.-
- UniProt
- Q72EF3, Q72EF4
- Ligands
- HEC, HQO, CA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C nitrite reductase, catalytic subunit nfra (EC 1.7.2.2) | protein | 495 | 41% helix, 6% strand | Q72EF3 |
| B | Cytochrome C nitrite reductase, catalytic subunit nfra (EC 1.7.2.2) | protein | 498 | 42% helix, 5% strand | Q72EF3 |
| C | NAPC/NIRT cytochrome C family protein (EC 1.10.2.-) | protein | 144 | 64% helix, 0% strand | Q72EF4 |
| D | Cytochrome C nitrite reductase, catalytic subunit nfra (EC 1.7.2.2) | protein | 494 | 40% helix, 6% strand | Q72EF3 |
| E | Cytochrome C nitrite reductase, catalytic subunit nfra (EC 1.7.2.2) | protein | 495 | 43% helix, 5% strand | Q72EF3 |
| F | NAPC/NIRT cytochrome C family protein (EC 1.10.2.-) | protein | 146 | 61% helix, 0% strand | Q72EF4 |
Ligands and binding sites
- HEC · Heme C · ligand · 28 copies · chains A, C, B, D, F, E
- HQO · 2-heptyl-4-hydroxy quinoline N-oxide · ligand · 2 copies · chains C, F
- CA · Calcium ion · metal · 8 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.90 | 0.93 | 103 | HEC |
| 2 | 1121 | 0.90 | 0.92 | 114 | HEC, CA |
| 3 | 811 | 0.90 | 0.93 | 115 | HEC |
| 4 | 343 | 0.86 | 0.95 | 64 | HEC, CA |
| 5 | 523 | 0.84 | 0.90 | 77 | HEC, HQO |
Interfaces
12 interfaces between chains.
- E–F · 1854 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1813 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1273 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1263 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1161 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 cofactor (heme c attachment).
Compared structures
- 2VR0 · Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO… · the same entry in another collection · chain F against F, TM-score 1.00
- Q72EF3 · AlphaFold monomer V2.0 prediction for cytochrome C nitrite reductase subunit nrfa (Q72EF3) · a predicted model of the same protein · chain E against A, TM-score 0.98
- Q72EF4 · AlphaFold monomer V2.0 prediction for cytochrome C nitrite reductase subunit nrfh (Q72EF4) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 Q72EF3
- Every structure of UniProt Q72EF4
- Elsewhere: RCSB PDB 2VR0 · PDBe 2VR0 · UniProt Q72EF3 · UniProt Q72EF4
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