Research workbench
Crystal structure of mycobacterium smegmatis CYP164A2 in ligand free state
Analyse Crystal structure of mycobacterium smegmatis CYP164A2 in ligand free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R9B
- Type
- protein
- Length
- 1,173 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 164A2
- EC
- 1.14.-.-
- UniProt
- A0R5U2
- Ligands
- HEM, D12, K, NA, PO4
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cytochrome P450 164A2 (EC 1.14.-.-) | protein | 391 | 58% helix, 10% strand | A0R5U2 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- D12 · Dodecane · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.86 | 0.86 | 81 | HEM, EDO, D12 |
| 2 | 1012 | 0.86 | 0.86 | 82 | HEM, EDO, D12 |
| 3 | 1046 | 0.85 | 0.86 | 81 | HEM, EDO, D12 |
| 4 | 903 | 0.80 | 0.82 | 91 | PO4, NA, EDO |
| 5 | 797 | 0.80 | 0.83 | 63 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1130 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 543 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3R9B · Crystal structure of Mycobacterium smegmatis CYP164A2 in ligand free state · 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 A0R5U2
- Elsewhere: RCSB PDB 3R9B · PDBe 3R9B · UniProt A0R5U2
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