MolNFT v1 · #122154 · protein
Macrolide 2'-phosphotransferase type I - complex with GDP and oleandomycin
5IGR: “Macrolide 2'-phosphotransferase type I - complex with GDP and oleandomycin”. X-ray diffraction, 3 ligands (GDP, ZIO, NH4), 1 pocket (best druggability 0.75). MolNFT v1 #122154 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5IGR
- Type
- protein
- Length
- 300 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrolide 2'-phosphotransferase
- UniProt
- Q47396
- Ligands
- GDP, ZIO, NH4
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrolide 2'-phosphotransferase | protein | 300 | 48% helix, 17% strand | Q47396 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- ZIO · (3S,5R,6S,7R,8R,11R,12S,13R,14S,15S)-6-hydroxy-5,7,8,11,13,15-hexamethyl-4,10-dioxo-14-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}-1,9-dioxaspiro[2.13]hexadec-12-yl 2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranoside · ligand · chains A
- NH4 · Ammonium ion · ion · 4 copies · chains A
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.75 | 0.78 | 74 | GDP, ZIO, NH4 |
Compared structures
- 5IGR · Macrolide 2'-phosphotransferase type I - complex with GDP and oleandomycin · 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 Q47396
- Elsewhere: RCSB PDB 5IGR · PDBe 5IGR · UniProt Q47396
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