Research workbench
Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with unsaturated trigalacturonic acid
Analyse Crystal structure of bacterial chemotaxis-dependent pectin-binding protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VEW
- Type
- protein
- Length
- 1,218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SPH1118
- Ligands
- GAD, ADA
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SPH1118 | protein | 609 | 34% helix, 21% strand | — |
Ligands and binding sites
- GAD · 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid · ligand · 2 copies · chains A, B
- ADA · alpha-D-galactopyranuronic acid · sugar · 4 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.86 | 0.88 | 101 | ADA, GAD, GOL |
| 2 | 433 | 0.82 | 0.90 | 46 | ADA, GAD, GOL |
| 3 | 244 | 0.82 | 0.94 | 41 | empty |
| 4 | 588 | 0.80 | 0.86 | 65 | empty |
| 5 | 621 | 0.65 | 0.75 | 66 | TLA |
Interfaces
1 interface between chains.
- A–B · 1512 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7VEW · Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in… · 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 7VEW · PDBe 7VEW
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