Research workbench
Cytochrome P450-153 from pseudomonas sp. 19-rlim
Analyse Cytochrome P450-153 from pseudomonas sp. 19-rlim in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HQD
- Type
- protein
- Length
- 1,241 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- UniProt
- G3LGZ6
- Ligands
- HEM, SRT
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 | protein | 414 | 51% helix, 10% strand | G3LGZ6 |
| B | Cytochrome P450 | protein | 412 | 51% helix, 10% strand | G3LGZ6 |
| C | Cytochrome P450 | protein | 415 | 51% helix, 10% strand | G3LGZ6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- SRT · S,R meso-tartaric acid · ligand · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.86 | 0.93 | 52 | HEM, PGE |
| 2 | 444 | 0.86 | 0.93 | 54 | HEM, PGE |
| 3 | 421 | 0.86 | 0.93 | 54 | HEM, PGE |
| 4 | 1063 | 0.85 | 0.86 | 104 | empty |
| 5 | 67 | 0.71 | 0.96 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 973 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 972 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 258 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6HQD · Cytochrome P450-153 from Pseudomonas sp. 19-rlim · 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 G3LGZ6
- Elsewhere: RCSB PDB 6HQD · PDBe 6HQD · UniProt G3LGZ6
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