MolNFT v1 · #174799 · protein
Crystal structure of beta-glycosides-binding protein (W41A) of ABC transporter in an open state (form I)
7C6X · Sugar ABC transporter, periplasmic sugar-binding protein: “Crystal structure of beta-glycosides-binding protein (W41A) of ABC transporter in an open state (form I)”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability…
- PDB
- 7C6X
- Type
- protein
- Length
- 4,959 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter, periplasmic sugar-binding protein
- UniProt
- Q53W80
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, I, J, K, L | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 413 | 49% helix, 16% strand | Q53W80 |
| G | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 416 | 49% helix, 16% strand | Q53W80 |
Ligands and binding sites
- CL · Chloride ion · ion · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PGE · Triethylene glycol · additive · 4 copies · chains F, I, G, H, K, L
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C, D, F, I
- EDO · 1,2-ethanediol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.83 | 0.84 | 96 | PGE |
| 2 | 1058 | 0.83 | 0.84 | 107 | PGE, PEG |
| 3 | 530 | 0.78 | 0.85 | 51 | empty |
| 4 | 533 | 0.77 | 0.84 | 55 | EDO |
| 5 | 717 | 0.77 | 0.82 | 70 | PEG |
Interfaces
20 interfaces between chains.
- E–J · 1746 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1687 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1671 Ų buried · 23 hydrogen bonds · protein-protein
- F–I · 1670 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1643 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7C6X · Crystal structure of beta-glycosides-binding protein (W41A) of ABC transporter in an open… · 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 7C6X · PDBe 7C6X · UniProt Q53W80
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