MolNFT v1 · #33966 · protein
Crystal structure of cytochrome cl from hyphomicrobium denitrificans
2D0W: “Crystal structure of cytochrome cl from hyphomicrobium denitrificans”. X-ray diffraction, 2 ligands (HEM, ZN), 5 pockets (best druggability 0.63). MolNFT v1 #33966 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2D0W
- Type
- protein
- Length
- 336 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome cl
- UniProt
- Q4AE24
- Ligands
- HEM, ZN
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome cl | protein | 168 | 46% helix, 1% strand | Q4AE24 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 10 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.63 | 0.83 | 30 | ZN, HEM |
| 2 | 174 | 0.62 | 0.83 | 26 | HEM |
| 3 | 304 | 0.61 | 0.79 | 35 | empty |
| 4 | 138 | 0.44 | 0.76 | 22 | empty |
| 5 | 53 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 231 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide (heme attachment, disulfide).
Compared structures
- 2D0W · Crystal structure of cytochrome cL from Hyphomicrobium denitrificans · the same entry in another collection · chain A against A, TM-score 1.00
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 Q4AE24
- Elsewhere: RCSB PDB 2D0W · PDBe 2D0W · UniProt Q4AE24
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