MolNFT v1 · #148093 · protein
Putative sugar aminotransferase SPR1654 from streptococcus pneumoniae, plp-form
6EWQ · Putative capsular polysaccharide biosynthesis protein: “Putative sugar aminotransferase SPR1654 from streptococcus pneumoniae, plp-form”. X-ray diffraction, 1 ligand (PLP), 17 pockets (best druggability 0.79). MolNFT v1 #148093 on…
- PDB
- 6EWQ
- Type
- protein
- Length
- 1,589 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative capsular polysaccharide biosynthesis protein
- UniProt
- A0A0H2URM1
- Ligands
- PLP
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative capsular polysaccharide biosynthesis protein | protein | 401 | 42% helix, 16% strand | A0A0H2URM1 |
| B | Putative capsular polysaccharide biosynthesis protein | protein | 392 | 41% helix, 16% strand | A0A0H2URM1 |
| C | Putative capsular polysaccharide biosynthesis protein | protein | 402 | 42% helix, 16% strand | A0A0H2URM1 |
| D | Putative capsular polysaccharide biosynthesis protein | protein | 394 | 41% helix, 16% strand | A0A0H2URM1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.79 | 0.95 | 24 | empty |
| 2 | 176 | 0.78 | 0.94 | 23 | empty |
| 3 | 730 | 0.74 | 0.80 | 71 | PLP |
| 4 | 68 | 0.74 | 0.99 | 21 | empty |
| 5 | 67 | 0.73 | 0.98 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2631 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2606 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 208 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 168 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 125 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6EWQ · Putative sugar aminotransferase Spr1654 from Streptococcus pneumoniae, PLP-form · 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 A0A0H2URM1
- Elsewhere: RCSB PDB 6EWQ · PDBe 6EWQ · UniProt A0A0H2URM1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.