Research workbench
Crystal structure of a putative oligosaccharide periplasmic-binding protein from synechococcus sp. MITS9220
Analyse Crystal structure of a putative oligosaccharide periplasmic-binding protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WPN
- Type
- protein
- Length
- 789 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Substrate-binding protein
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Substrate-binding protein | protein | 395 | 51% helix, 14% strand | — |
| B | Substrate-binding protein | protein | 394 | 51% helix, 16% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.74 | 0.84 | 50 | empty |
| 2 | 373 | 0.72 | 0.84 | 56 | empty |
| 3 | 588 | 0.70 | 0.78 | 65 | empty |
| 4 | 149 | 0.58 | 0.83 | 29 | empty |
| 5 | 140 | 0.41 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1671 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 6WPN · Crystal structure of a putative oligosaccharide periplasmic-binding protein from… · 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
- Elsewhere: RCSB PDB 6WPN · PDBe 6WPN
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