MolNFT v1 · #14579 · protein
Key role of phenylalanine 20 in cytochrome C3: structure, stability and function studies
1MDV: “Key role of phenylalanine 20 in cytochrome C3: structure, stability and function studies”. X-ray diffraction, 1 ligand (HEM), 2 pockets (best druggability 0.84). MolNFT v1 #14579 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1MDV
- Type
- protein
- Length
- 201 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C3
- UniProt
- P00131
- Ligands
- HEM
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C3 | protein | 101 | 30% helix, 10% strand | P00131 |
| B | Cytochrome C3 | protein | 100 | 24% helix, 6% strand | P00131 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B
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 | 774 | 0.84 | 0.86 | 73 | HEM |
| 2 | 168 | 0.67 | 0.87 | 25 | HEM |
Interfaces
1 interface between chains.
- A–B · 759 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (heme attachment).
Compared structures
- 1MDV · Key role of phenylalanine 20 in cytochrome C3: structure, stability and function studies · the same entry in another collection · chain B against B, TM-score 1.00
- P00131 · AlphaFold monomer V2.0 prediction for cytochrome C3 (P00131) · a predicted model of the same protein · chain A against A, TM-score 0.89
- 1GX7 · Best model of the electron transfer complex between cytochrome C3 and [fe]-hydrogenase · a predicted model of the same protein · chain A against E, TM-score 0.79
- 1GX7 · Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase · a predicted model of the same protein · chain A against E, TM-score 0.79
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 P00131
- Elsewhere: RCSB PDB 1MDV · PDBe 1MDV · UniProt P00131
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