Research workbench
Nitric oxide reductase from roseobacter denitrificans (rdnor)
Analyse Nitric oxide reductase from roseobacter denitrificans (rdnor) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XYD
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric-oxide reductase subunit B; Norc-like protein
- EC
- 1.7.2.5
- UniProt
- Q16A04, Q16A03
- Ligands
- HEM, UNL, HEC, CA, FE, CU
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric-oxide reductase subunit B (EC 1.7.2.5) | protein | 445 | 79% helix, 0% strand | Q16A04 |
| B | Norc-like protein (EC 1.7.2.5) | protein | 145 | 57% helix, 3% strand | Q16A03 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- UNL · Unknown ligand · ligand · chains A
- HEC · Heme C · ligand · chains A, B
- CA · Calcium ion · metal · chains A, B
- FE · Fe (III) ion · metal · chains A
- CU · Copper (II) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.88 | 0.92 | 104 | HEM, UNL |
| 2 | 254 | 0.75 | 0.88 | 35 | HEC |
| 3 | 226 | 0.55 | 0.77 | 21 | empty |
| 4 | 78 | 0.35 | 0.76 | 16 | empty |
| 5 | 58 | 0.33 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3336 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (heme c attachment).
Compared structures
- 4XYD · Nitric oxide reductase from Roseobacter denitrificans (RdNOR) · the same entry in another collection · chain A against A, 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 Q16A04
- Every structure of UniProt Q16A03
- Elsewhere: RCSB PDB 4XYD · PDBe 4XYD · UniProt Q16A04 · UniProt Q16A03
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