Research workbench
Nitrosyl complex of the D121Q variant of cytochrome C prime from alcaligenes xylosoxidans
Analyse Nitrosyl complex of the D121Q variant of cytochrome C prime from alcaligenes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AGF
- Type
- protein
- Length
- 125 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C prime
- UniProt
- P00138
- Ligands
- HEC, NO, SO4
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C prime | protein | 125 | 74% helix, 2% strand | P00138 |
Ligands and binding sites
- HEC · Heme C · ligand · chains A
- NO · Nitric oxide · ion · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.66 | 0.83 | 30 | HEC, NO |
Modifications
Observed in the structure: 2 cofactor, 1 modified (heme c attachment, cyclization).
Compared structures
- 5AGF · Nitrosyl complex of the D121Q variant of cytochrome c prime from Alcaligenes xylosoxidans · the same entry in another collection · chain A against A, TM-score 1.00
- P00138 · AlphaFold monomer V2.0 prediction for cytochrome C' (P00138) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00138
- Elsewhere: RCSB PDB 5AGF · PDBe 5AGF · UniProt P00138
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