MolNFT v2 · #137405 · protein
Crystal structure of macrolide 2'-phosphotransferase MphH from Brachybacterium faecium in complex with azithromycin
5UXD: “Crystal structure of macrolide 2'-phosphotransferase MphH from Brachybacterium faecium in complex with…”. X-ray diffraction at 1.7, 3 ligands (ZIT, CL, SO4), 4 pockets (best druggability 0.76). MolNFT v2 #137405 on GenesisL1: 3D…
- PDB
- 5UXD
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Brachybacterium faecium (strain ATCC 43885 / DSM 4810 / NCIB 9860)
- Molecule
- Macrolide 2'-phosphotransferase MphH
- UniProt
- C7MEP1
- Ligands
- ZIT, CL, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.7 · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrolide 2'-phosphotransferase MphH | protein | 300 | 47% helix, 19% strand | C7MEP1 |
| B | Macrolide 2'-phosphotransferase MphH | protein | 299 | 48% helix, 17% strand | C7MEP1 |
Ligands and binding sites
- ZIT · Azithromycin · ligand · 3 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.76 | 0.78 | 66 | ZIT, CL |
| 2 | 467 | 0.62 | 0.76 | 34 | CL |
| 3 | 348 | 0.60 | 0.77 | 40 | empty |
| 4 | 371 | 0.60 | 0.76 | 36 | CL |
Interfaces
1 interface between chains.
- A–B · 665 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5UXD · Crystal structure of macrolide 2'-phosphotransferase mphh from brachybacterium faecium in… · 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 C7MEP1
- Elsewhere: RCSB PDB 5UXD · PDBe 5UXD · UniProt C7MEP1
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