MolNFT v1 · #120302 · protein
Crystal structure of the glycosyltransferase glye in streptococcus pneumoniae TIGR4
5GVV · Glycosyl transferase family 8: “Crystal structure of the glycosyltransferase glye in streptococcus pneumoniae TIGR4”. X-ray diffraction, 2 ligands (UDP, MN), 7 pockets (best druggability 0.82). MolNFT v1 #120302 on GenesisL1: 3D…
- PDB
- 5GVV
- Type
- protein
- Length
- 777 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl transferase family 8
- UniProt
- A0A0Y1PI62
- Ligands
- UDP, MN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase family 8 | protein | 392 | 38% helix, 19% strand | A0A0Y1PI62 |
| F | Glycosyl transferase family 8 | protein | 385 | 38% helix, 20% strand | A0A0Y1PI62 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, F
- MN · Manganese (II) ion · metal · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.82 | 0.96 | 29 | empty |
| 2 | 544 | 0.65 | 0.76 | 51 | empty |
| 3 | 582 | 0.65 | 0.76 | 52 | empty |
| 4 | 420 | 0.61 | 0.76 | 48 | UDP |
| 5 | 305 | 0.58 | 0.77 | 31 | UDP |
Interfaces
1 interface between chains.
- A–F · 2026 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5GVV · Crystal structure of the glycosyltransferase GlyE in Streptococcus pneumoniae TIGR4 · 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 A0A0Y1PI62
- Elsewhere: RCSB PDB 5GVV · PDBe 5GVV · UniProt A0A0Y1PI62
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