Research workbench
Crystal structure of a periplasmic sugar ABC transporter from thermotoga maritima
Analyse Crystal structure of a periplasmic sugar ABC transporter from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QVC
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter, periplasmic sugar-binding protein
- UniProt
- Q9WXW9
- Ligands
- BGC
- Pockets
- 15 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 302 | 45% helix, 23% strand | Q9WXW9 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.53 | 0.82 | 21 | empty |
| 2 | 86 | 0.50 | 0.83 | 18 | empty |
| 3 | 82 | 0.47 | 0.81 | 18 | empty |
| 4 | 98 | 0.46 | 0.80 | 19 | empty |
| 5 | 153 | 0.46 | 0.76 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 861 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 471 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 450 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 444 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 2QVC · Crystal structure of a periplasmic sugar ABC transporter from Thermotoga maritima · 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 Q9WXW9
- Elsewhere: RCSB PDB 2QVC · PDBe 2QVC · UniProt Q9WXW9
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