MolNFT v1 · #120272 · protein
Complex of cytochrome CD1 nitrite reductase and nitric oxide reductase in denitrification of pseudomonas aeruginosa
5GUW · Nitric oxide reductase subunit C: “Complex of cytochrome CD1 nitrite reductase and nitric oxide reductase in denitrification of pseudomonas…”. X-ray diffraction, 8 ligands (HEC, HEM, 10M), 19 pockets (best druggability 0.90). MolNFT…
- PDB
- 5GUW
- Type
- protein
- Length
- 2,258 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide reductase subunit C; Nitric oxide reductase subunit B; Nitrite reductase
- EC
- 1.7.2.5, 1.7.2.1, 1.7.99.1
- UniProt
- Q59646, Q59647, P24474
- Ligands
- HEC, HEM, 10M, DHE, CA, FE, O, CL
- Pockets
- 19 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitric oxide reductase subunit C | protein | 142 | 60% helix, 4% strand | Q59646 |
| B, D | Nitric oxide reductase subunit B (EC 1.7.2.5) | protein | 449 | 78% helix, 0% strand | Q59647 |
| M, N | Nitrite reductase (EC 1.7.2.1, 1.7.99.1) | protein | 538 | 14% helix, 37% strand | P24474 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D, M, N
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 10M · decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside · ligand · 3 copies · chains A, B, C, D
- DHE · Heme D · ligand · 2 copies · chains M, N
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 2 copies · chains B, D
- O · Oxygen atom · ion · 2 copies · chains B, D
- CL · Chloride ion · ion · 2 copies · chains M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.90 | 0.93 | 110 | CA, HEM, O |
| 2 | 671 | 0.89 | 0.94 | 91 | HEM, O |
| 3 | 1068 | 0.86 | 0.87 | 117 | HEC, DHE |
| 4 | 1120 | 0.85 | 0.85 | 118 | HEC, DHE |
| 5 | 473 | 0.84 | 0.91 | 50 | CL |
Interfaces
5 interfaces between chains.
- C–D · 3442 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3408 Ų buried · 43 hydrogen bonds · protein-protein
- M–N · 3255 Ų buried · 34 hydrogen bonds · protein-protein
- A–N · 418 Ų buried · 3 hydrogen bonds · protein-protein
- C–M · 415 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 5GUW · Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification… · the same entry in another collection · chain N against N, TM-score 1.00
- Q59647 · AlphaFold monomer V2.0 prediction for nitric oxide reductase subunit B (Q59647) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q59646 · AlphaFold monomer V2.0 prediction for nitric oxide reductase subunit C (Q59646) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P24474 · AlphaFold monomer V2.0 prediction for nitrite reductase (P24474) · a predicted model of the same protein · chain M 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 Q59646
- Every structure of UniProt Q59647
- Every structure of UniProt P24474
- Elsewhere: RCSB PDB 5GUW · PDBe 5GUW · UniProt Q59646 · UniProt Q59647 · UniProt P24474
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