Research workbench
W. succinogenes nrfa Y218F nitrite complex
Analyse W. succinogenes nrfa Y218F nitrite complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BNH
- Type
- protein
- Length
- 471 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C-552
- EC
- 1.7.2.2
- UniProt
- Q9S1E5
- Ligands
- HEM, Y1, CA, NO2, SO4
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C-552 (EC 1.7.2.2) | protein | 471 | 52% helix, 8% strand | Q9S1E5 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A
- Y1 · Yttrium ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- NO2 · Nitrite ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.87 | 0.88 | 108 | NO2, HEM |
| 2 | 68 | 0.68 | 0.94 | 27 | empty |
Modifications
Observed in the structure: 10 cofactor (heme attachment).
Compared structures
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 Q9S1E5
- Elsewhere: RCSB PDB 3BNH · PDBe 3BNH · UniProt Q9S1E5
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