Research workbench
Structural and functional characterization of olep in complex with 6DEB in peg
Analyse Structural and functional characterization of olep in complex with 6DEB in peg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MNV
- Type
- protein
- Length
- 3,427 residues
- Chains
- 9
- 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 · 7 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P-450 | protein | 397 | 50% helix, 10% strand | Q59819 |
| B, D | Cytochrome P-450 | protein | 394 | 50% helix, 10% strand | Q59819 |
| C | Cytochrome P-450 | protein | 396 | 51% helix, 11% strand | Q59819 |
| E | Cytochrome P-450 | protein | 390 | 48% helix, 9% strand | Q59819 |
| F, H | Cytochrome P-450 | protein | 395 | 47% helix, 8% strand | Q59819 |
| G | Cytochrome P-450 | protein | 380 | 47% helix, 10% strand | Q59819 |
| I | Cytochrome P-450 | protein | 286 | 57% helix, 4% strand | Q59819 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I
- DEB · 6-deoxyerythronolide B · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I
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 | 808 | 0.88 | 0.90 | 64 | HEM, DEB |
| 2 | 794 | 0.87 | 0.90 | 68 | HEM, DEB |
| 3 | 875 | 0.82 | 0.84 | 86 | HEM, DEB |
| 4 | 956 | 0.82 | 0.83 | 80 | HEM, DEB |
| 5 | 1018 | 0.82 | 0.83 | 77 | HEM, DEB |
Interfaces
14 interfaces between chains.
- C–E · 681 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 666 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 638 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 628 Ų buried · 10 hydrogen bonds · protein-protein
- C–I · 582 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5MNV · Structural and functional characterization of OleP in complex with 6DEB in PEG · 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 5MNV · PDBe 5MNV · UniProt Q59819
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