MolNFT v1 · #76440 · protein
Structure of streptococcus parasangunini GTF3 glycosyltransferase
3QKW · Nucleotide sugar synthetase-like protein: “Structure of streptococcus parasangunini GTF3 glycosyltransferase”. X-ray diffraction, 1 ligand (UDP), 9 pockets (best druggability 0.79). MolNFT v1 #76440 on GenesisL1: 3D structure…
- PDB
- 3QKW
- Type
- protein
- Length
- 1,307 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide sugar synthetase-like protein
- UniProt
- B5A7L9
- Ligands
- UDP
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleotide sugar synthetase-like protein | protein | 328 | 41% helix, 20% strand | B5A7L9 |
| B | Nucleotide sugar synthetase-like protein | protein | 324 | 44% helix, 20% strand | B5A7L9 |
| C | Nucleotide sugar synthetase-like protein | protein | 329 | 42% helix, 20% strand | B5A7L9 |
| D | Nucleotide sugar synthetase-like protein | protein | 326 | 40% helix, 20% strand | B5A7L9 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
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 | 456 | 0.79 | 0.86 | 67 | UDP |
| 2 | 381 | 0.78 | 0.88 | 62 | UDP |
| 3 | 432 | 0.77 | 0.86 | 44 | empty |
| 4 | 373 | 0.75 | 0.86 | 41 | empty |
| 5 | 256 | 0.74 | 0.88 | 41 | UDP |
Interfaces
6 interfaces between chains.
- B–C · 1133 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1131 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1123 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1068 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 357 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 B5A7L9
- Elsewhere: RCSB PDB 3QKW · PDBe 3QKW · UniProt B5A7L9
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