MolNFT v1 · #164523 · protein
Crystal structure of CYP124 in complex with SQ109
6T0J · Methyl-branched lipid omega-hydroxylase: “Crystal structure of CYP124 in complex with SQ109”. X-ray diffraction, 3 ligands (HEM, RWZ, MG), 5 pockets (best druggability 0.89). MolNFT v1 #164523 on GenesisL1: 3D structure, binding…
- PDB
- 6T0J
- Type
- protein
- Length
- 429 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-branched lipid omega-hydroxylase
- EC
- 1.14.15.14, 1.14.15.28
- UniProt
- P9WPP3
- Ligands
- HEM, RWZ, MG
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-branched lipid omega-hydroxylase (EC 1.14.15.14, 1.14.15.28) | protein | 429 | 50% helix, 11% strand | P9WPP3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- RWZ · N-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-N'-[(1R,3S,5R, 7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]ethane-1,2-diamine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- FMT · Formic acid · additive · 4 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.89 | 0.94 | 73 | HEM, RWZ |
| 2 | 171 | 0.72 | 0.90 | 34 | empty |
| 3 | 55 | 0.37 | 0.80 | 17 | empty |
| 4 | 55 | 0.34 | 0.78 | 18 | empty |
| 5 | 67 | 0.34 | 0.77 | 15 | empty |
Compared structures
- 6T0J · Crystal structure of CYP124 in complex with SQ109 · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPP3 · AlphaFold monomer V2.0 prediction for methyl-branched lipid omega- hydroxylase (P9WPP3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P9WPP3
- Elsewhere: RCSB PDB 6T0J · PDBe 6T0J · UniProt P9WPP3
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