MolNFT v1 · #127142 · protein
Structural and functional characterization of olep in complex with 6DEB in sodium formate
5MNS · Cytochrome P-450: “Structural and functional characterization of olep in complex with 6DEB in sodium formate”. X-ray diffraction, 2 ligands (HEM, DEB), 20 pockets (best druggability 0.88). MolNFT v1 #127142 on GenesisL1: 3D…
- PDB
- 5MNS
- Type
- protein
- Length
- 2,368 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P-450
- UniProt
- Q59819
- Ligands
- HEM, DEB
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cytochrome P-450 | protein | 395 | 51% helix, 10% strand | Q59819 |
| F | Cytochrome P-450 | protein | 393 | 49% 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
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 | 761 | 0.88 | 0.91 | 64 | HEM, DEB |
| 2 | 778 | 0.87 | 0.90 | 69 | HEM, DEB |
| 3 | 833 | 0.87 | 0.89 | 72 | HEM, DEB |
| 4 | 794 | 0.87 | 0.90 | 71 | HEM, DEB |
| 5 | 752 | 0.86 | 0.89 | 65 | HEM, DEB |
Interfaces
5 interfaces between chains.
- D–E · 805 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 719 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 577 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 557 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 93 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (heme attachment).
Compared structures
- 5MNS · Structural and functional characterization of OleP in complex with 6DEB in sodium formate · 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 5MNS · PDBe 5MNS · UniProt Q59819
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