MolNFT v1 · #174771 · protein
Crystal structure of beta-glycosides-binding protein of ABC transporter in an open state (form II)
7C64 · Sugar ABC transporter, periplasmic sugar-binding protein: “Crystal structure of beta-glycosides-binding protein of ABC transporter in an open state (form II)”. X-ray diffraction, 4 ligands (MRY, CL, CO2), 5 pockets (best…
- PDB
- 7C64
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter, periplasmic sugar-binding protein
- UniProt
- Q53W80
- Ligands
- MRY, CL, CO2, PO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 415 | 51% helix, 17% strand | Q53W80 |
Ligands and binding sites
- MRY · Meso-erythritol · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, B
- CO2 · Carbon dioxide · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.84 | 0.86 | 115 | PEG, PGE, PG4, P33 |
| 2 | 232 | 0.56 | 0.78 | 34 | empty |
| 3 | 194 | 0.55 | 0.79 | 29 | empty |
| 4 | 129 | 0.51 | 0.80 | 21 | empty |
| 5 | 90 | 0.47 | 0.81 | 16 | CL |
Interfaces
1 interface between chains.
- A–B · 1666 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C64 · Crystal structure of beta-glycosides-binding protein of ABC transporter in an open state… · 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 Q53W80
- Elsewhere: RCSB PDB 7C64 · PDBe 7C64 · UniProt Q53W80
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