MolNFT v1 · #171837 · protein
Crystal structure of olep-OLEANDOLIDE(DEO) bound to L-rhamnose
6ZI7 · Cytochrome P-450: “Crystal structure of olep-OLEANDOLIDE(DEO) bound to L-rhamnose”. X-ray diffraction, 4 ligands (HEM, QR8, RAM), 20 pockets (best druggability 0.87). MolNFT v1 #171837 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZI7
- Type
- protein
- Length
- 2,391 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P-450
- UniProt
- Q59819
- Ligands
- HEM, QR8, 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 | Cytochrome P-450 | protein | 396 | 52% helix, 10% strand | Q59819 |
| B, C, D | Cytochrome P-450 | protein | 400 | 51% helix, 10% strand | Q59819 |
| E | Cytochrome P-450 | protein | 397 | 51% helix, 10% strand | Q59819 |
| F | Cytochrome P-450 | protein | 398 | 50% helix, 10% strand | Q59819 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- QR8 · (3~{R},4~{S},5~{R},6~{S},7~{S},9~{S},11~{R},12~{S}, 13~{R},14~{R})-3,5,7,9,11,13,14-heptamethyl-4,6,12-tris(oxidanyl)-1-oxacyclotetradecane-2,10-dione · ligand · 6 copies · chains A, B, C, D, E, F
- RAM · alpha-L-rhamnopyranose · sugar · 3 copies · chains A, B, D
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 214 copies · chains A, D, B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.87 | 0.90 | 66 | HEM, QR8, FMT |
| 2 | 774 | 0.87 | 0.90 | 67 | HEM, QR8, RAM, FMT |
| 3 | 740 | 0.87 | 0.90 | 64 | HEM, QR8 |
| 4 | 790 | 0.87 | 0.90 | 68 | HEM, QR8, FMT |
| 5 | 1007 | 0.86 | 0.87 | 99 | HEM, QR8, RAM, FMT |
Interfaces
5 interfaces between chains.
- D–E · 800 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 731 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 695 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 660 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 89 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZI7 · Crystal structure of OleP-oleandolide(DEO) 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 6ZI7 · PDBe 6ZI7 · UniProt Q59819
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