MolNFT v1 · #8204 · protein
Crystal structure of oxidized cytochrome C'' from methylophilus methylotrophus
1GU2: “Crystal structure of oxidized cytochrome C'' from methylophilus methylotrophus”. X-ray diffraction, 1 ligand (HEC), 5 pockets (best druggability 0.69). MolNFT v1 #8204 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1GU2
- Type
- protein
- Length
- 247 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C''
- UniProt
- Q9RQB9
- Ligands
- HEC
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C'' | protein | 124 | 49% helix, 6% strand | Q9RQB9 |
| B | Cytochrome C'' | protein | 123 | 48% helix, 7% strand | Q9RQB9 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.69 | 0.81 | 36 | HEC |
| 2 | 296 | 0.67 | 0.82 | 30 | HEC |
| 3 | 106 | 0.42 | 0.77 | 20 | empty |
| 4 | 88 | 0.36 | 0.75 | 20 | empty |
| 5 | 88 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 1GU2 · Crystal structure of oxidized cytochrome c'' from Methylophilus methylotrophus · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RQB9 · AlphaFold monomer V2.0 prediction for cytochrome C'' (Q9RQB9) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9RQB9
- Elsewhere: RCSB PDB 1GU2 · PDBe 1GU2 · UniProt Q9RQB9
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