Research workbench
Crystal structure of a putative oligosaccharide periplasmic-binding protein from synechococcus sp. MITS9220 in complex with zinc
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
- 6WPM
- Type
- protein
- Length
- 401 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Substrate-binding protein
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Substrate-binding protein | protein | 401 | 51% helix, 15% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.78 | 0.81 | 56 | ZN, SO4 |
| 2 | 109 | 0.77 | 0.96 | 26 | empty |
| 3 | 180 | 0.48 | 0.75 | 20 | empty |
| 4 | 91 | 0.35 | 0.74 | 15 | empty |
| 5 | 63 | 0.30 | 0.74 | 13 | empty |
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 6WPM · 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 6WPM · PDBe 6WPM
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