MolNFT v1 · #171833 · protein
Crystal structure of olep-6DEB bound to L-rhamnose
6ZI3 · Cytochrome P-450: “Crystal structure of olep-6DEB bound to L-rhamnose”. X-ray diffraction, 4 ligands (HEM, DEB, RAM), 20 pockets (best druggability 0.87). MolNFT v1 #171833 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6ZI3
- Type
- protein
- Length
- 2,385 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P-450
- UniProt
- Q59819
- Ligands
- HEM, DEB, RAM, NA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Cytochrome P-450 | protein | 397 | 51% helix, 10% strand | Q59819 |
| B | Cytochrome P-450 | protein | 403 | 50% helix, 9% strand | Q59819 |
| D | Cytochrome P-450 | protein | 396 | 51% helix, 10% strand | Q59819 |
| E | Cytochrome P-450 | protein | 395 | 51% helix, 10% strand | Q59819 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- DEB · 6-deoxyerythronolide B · ligand · 6 copies · chains A, B, C, D, E, F
- RAM · alpha-L-rhamnopyranose · sugar · 7 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 203 copies · chains A, D, B, F, C, E
- GOL · Glycerol · additive · 6 copies · chains B, C, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.87 | 0.90 | 66 | HEM, DEB, GOL, FMT |
| 2 | 801 | 0.87 | 0.90 | 66 | HEM, DEB, RAM |
| 3 | 814 | 0.87 | 0.90 | 64 | HEM, DEB, RAM, FMT |
| 4 | 802 | 0.87 | 0.89 | 65 | HEM, DEB, RAM, FMT |
| 5 | 840 | 0.87 | 0.89 | 69 | HEM, DEB, RAM, GOL, FMT |
Interfaces
5 interfaces between chains.
- B–C · 795 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 759 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 700 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 572 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZI3 · Crystal structure of OleP-6DEB bound to L-rhamnose · 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 Q59819
- Elsewhere: RCSB PDB 6ZI3 · PDBe 6ZI3 · UniProt Q59819
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