Research workbench
Putative sugar aminotransferase SPR1654 from streptococcus pneumoniae, pmp-form
Analyse Putative sugar aminotransferase SPR1654 from streptococcus pneumoniae, pmp-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EWR
- Type
- protein
- Length
- 1,592 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative capsular polysaccharide biosynthesis protein
- UniProt
- A0A0H2URM1
- Ligands
- PMP
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative capsular polysaccharide biosynthesis protein | protein | 399 | 42% helix, 16% strand | A0A0H2URM1 |
| B | Putative capsular polysaccharide biosynthesis protein | protein | 396 | 43% helix, 16% strand | A0A0H2URM1 |
| C | Putative capsular polysaccharide biosynthesis protein | protein | 400 | 43% helix, 16% strand | A0A0H2URM1 |
| D | Putative capsular polysaccharide biosynthesis protein | protein | 397 | 43% helix, 16% strand | A0A0H2URM1 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.80 | 0.96 | 23 | empty |
| 2 | 774 | 0.75 | 0.80 | 80 | PMP |
| 3 | 632 | 0.74 | 0.81 | 70 | PMP |
| 4 | 763 | 0.74 | 0.79 | 71 | PMP |
| 5 | 65 | 0.74 | 0.99 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2603 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2579 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 202 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 168 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 126 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EWR · Putative sugar aminotransferase Spr1654 from Streptococcus pneumoniae, PMP-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 6EWR · PDBe 6EWR · UniProt A0A0H2URM1
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