Research workbench
Crystal structure of mycinamicin VIII C21 methyl hydroxylase mycci from micromonospora griseorubida bound to mycinamicin VIII
Analyse Crystal structure of mycinamicin VIII C21 methyl hydroxylase mycci from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FOI
- Type
- protein
- Length
- 777 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mycinamicin VIII C21 methyl hydroxylase
- EC
- 1.14.-.-
- UniProt
- Q83WF5
- Ligands
- SPD, HEM, MY8
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mycinamicin VIII C21 methyl hydroxylase (EC 1.14.-.-) | protein | 389 | 51% helix, 10% strand | Q83WF5 |
| B | Mycinamicin VIII C21 methyl hydroxylase (EC 1.14.-.-) | protein | 388 | 52% helix, 10% strand | Q83WF5 |
Ligands and binding sites
- SPD · Spermidine · ligand · 3 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MY8 · Mycinamicin VIII · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.87 | 0.88 | 81 | HEM, MY8, GOL |
| 2 | 1029 | 0.87 | 0.88 | 83 | HEM, MY8 |
| 3 | 586 | 0.73 | 0.80 | 68 | empty |
| 4 | 373 | 0.64 | 0.79 | 45 | empty |
| 5 | 128 | 0.53 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 608 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5FOI · Crystal structure of mycinamicin VIII C21 methyl hydroxylase MycCI from Micromonospora… · the same entry in another collection · chain A against A, TM-score 1.00
- Q83WF5 · AlphaFold monomer V2.0 prediction for mycinamicin VIII C21 methyl hydroxylase (Q83WF5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q83WF5
- Elsewhere: RCSB PDB 5FOI · PDBe 5FOI · UniProt Q83WF5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.