Research workbench
Complex of cytochrome CD1 nitrite reductase and nitric oxide reductase in denitrification of pseudomonas aeruginosa
Analyse Complex of cytochrome CD1 nitrite reductase and nitric oxide reductase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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