MolNFT v1 · #37744 · protein
Solution structure of the complex between yeast iso-1-cytochrome C and yeast cytochrome C peroxidase
2GB8: “Solution structure of the complex between yeast iso-1-cytochrome C and yeast cytochrome C peroxidase”. Solution nmr, 2 ligands (HEM, HEC), 4 pockets (best druggability 0.82). MolNFT v1 #37744 on GenesisL1: 3D structure, binding…
- PDB
- 2GB8
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase; Cytochrome C iso-1
- EC
- 1.11.1.5
- UniProt
- P00431, P00044
- Ligands
- HEM, HEC
- Pockets
- 4 · best druggability 0.82
Structure
solution nmr · 2 distinct chains · 47% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C peroxidase (EC 1.11.1.5) | protein | 294 | 50% helix, 7% strand | P00431 |
| B | Cytochrome C iso-1 | protein | 103 | 40% helix, 2% strand | P00044 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.82 | 0.89 | 46 | HEM |
| 2 | 261 | 0.78 | 0.91 | 31 | empty |
| 3 | 332 | 0.77 | 0.88 | 56 | HEC |
| 4 | 77 | 0.35 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (heme c attachment).
Compared structures
- 2GB8 · Solution structure of the complex between yeast iso-1-cytochrome c and yeast cytochrome c… · the same entry in another collection · chain A against A, TM-score 1.00
- P00431 · AlphaFold monomer V2.0 prediction for cytochrome C peroxidase, mitochondrial (P00431) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P00044 · AlphaFold monomer V2.0 prediction for cytochrome C isoform 1 (P00044) · a predicted model of the same protein · chain B 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 P00431
- Every structure of UniProt P00044
- Elsewhere: RCSB PDB 2GB8 · PDBe 2GB8 · UniProt P00431 · UniProt P00044
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.