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Crystal structure of the pneumococcal O-glcnac transferase gtfa in complex with udp and glcnac
Analyse Crystal structure of the pneumococcal O-glcnac transferase gtfa in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PQG
- Type
- protein
- Length
- 1,007 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase GTF1
- EC
- 2.4.1.-
- UniProt
- Q97P84
- Ligands
- UDP, NAG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase GTF1 (EC 2.4.1.-) | protein | 506 | 32% helix, 27% strand | Q97P84 |
| B | Glycosyltransferase GTF1 (EC 2.4.1.-) | protein | 501 | 33% helix, 28% strand | Q97P84 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.77 | 0.84 | 70 | UDP, NAG |
| 2 | 629 | 0.76 | 0.82 | 71 | UDP, NAG |
| 3 | 864 | 0.73 | 0.77 | 78 | empty |
| 4 | 288 | 0.66 | 0.82 | 47 | empty |
| 5 | 177 | 0.54 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1824 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4PQG · Crystal structure of the pneumococcal O-GlcNAc transferase GtfA in complex with UDP and… · 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 Q97P84
- Elsewhere: RCSB PDB 4PQG · PDBe 4PQG · UniProt Q97P84
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