Research workbench
Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor
Analyse Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R1I
- Type
- protein
- Length
- 1,223 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.24
- Source
- Mycobacterium tuberculosis H37Rv
- Molecule
- Steroid C26-monooxygenase
- EC
- 1.14.15.29
- UniProt
- P9WPP1
- Ligands
- HIH, HEM, SO4, CL
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.24 · 3 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Steroid C26-monooxygenase (EC 1.14.15.29) | protein | 411 | 49% helix, 11% strand | P9WPP1 |
| B | Steroid C26-monooxygenase (EC 1.14.15.29) | protein | 403 | 48% helix, 11% strand | P9WPP1 |
| C | Steroid C26-monooxygenase (EC 1.14.15.29) | protein | 409 | 50% helix, 11% strand | P9WPP1 |
Ligands and binding sites
- HIH · ethyl 1-(2-piperidin-4-ylethyl)-5-pyridin-4-yl-indole-2-carboxylate · ligand · 4 copies · chains A, B, C
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.87 | 0.89 | 84 | HEM, HIH, CL |
| 2 | 712 | 0.85 | 0.88 | 77 | HEM, HIH |
| 3 | 730 | 0.85 | 0.88 | 74 | HEM, HIH, CL |
| 4 | 1032 | 0.84 | 0.85 | 93 | empty |
| 5 | 105 | 0.53 | 0.83 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 637 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 449 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- P9WPP1 · AlphaFold monomer V2.0 prediction for steroid C26-monooxygenase (P9WPP1) · a predicted model of the same protein · chain B 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 P9WPP1
- Elsewhere: RCSB PDB 7R1I · PDBe 7R1I · UniProt P9WPP1
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