Research workbench
Structural and functional characterization of olep in complex with 6DEB in sodium formate
Analyse Structural and functional characterization of olep in complex with 6DEB in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.