Research workbench
Dominant form of the low-affinity complex of yeast cytochrome C and cytochrome C peroxidase
Analyse Dominant form of the low-affinity complex of yeast cytochrome C and cytochrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2N18
- Type
- protein
- Length
- 510 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase, mitochondrial; Cytochrome C iso-1
- EC
- 1.11.1.5
- UniProt
- P00431, P00044
- Ligands
- HEC, HEM
- Pockets
- 4 · best druggability 0.81
Structure
solution nmr · 3 distinct chains · 46% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 294 | 50% helix, 7% strand | P00431 |
| B | Cytochrome C iso-1 | protein | 108 | 43% helix, 2% strand | P00044 |
| C | Cytochrome C iso-1 | protein | 108 | 38% helix, 2% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B, C
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
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 | 967 | 0.81 | 0.83 | 90 | HEC |
| 2 | 388 | 0.79 | 0.88 | 44 | HEM |
| 3 | 556 | 0.74 | 0.82 | 64 | HEC |
| 4 | 88 | 0.40 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 316 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 182 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 disulfide (heme c attachment, disulfide).
Compared structures
- 2N18 · Dominant form of the low-affinity complex of yeast cytochrome c and 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 2N18 · PDBe 2N18 · UniProt P00431 · UniProt P00044
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