Research workbench
X-ray structure of mycobacterium tuberculosis cytochrome P450 CYP125 in complex with substrate cholest-4-en-3-one
Analyse X-ray structure of mycobacterium tuberculosis cytochrome P450 CYP125 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X5W
- Type
- protein
- Length
- 409 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cytochrome P450 125
- EC
- 1.14.-.-
- UniProt
- P63709
- Ligands
- K2B, HEM, SO4
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative cytochrome P450 125 (EC 1.14.-.-) | protein | 409 | 50% helix, 12% strand | P63709 |
Ligands and binding sites
- K2B · (8alpha,9beta)-cholest-4-en-3-one · ligand · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.86 | 0.90 | 73 | K2B, HEM |
| 2 | 103 | 0.39 | 0.76 | 21 | empty |
| 3 | 94 | 0.37 | 0.75 | 19 | empty |
Compared structures
- 2X5W · X-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP125 in complex with… · 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 P63709
- Elsewhere: RCSB PDB 2X5W · PDBe 2X5W · UniProt P63709
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