Research workbench
Crystal structure of E. COLI ygjk D324N complexed with melibiose
Analyse Crystal structure of E. COLI ygjk D324N complexed with melibiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W7X
- Type
- protein
- Length
- 1,520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein ygjk
- UniProt
- P42592
- Ligands
- GLC, GLA, CA
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein ygjk | protein | 760 | 34% helix, 24% strand | P42592 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.72 | 0.82 | 47 | GLC, GLA |
| 2 | 409 | 0.71 | 0.82 | 45 | GLC, GLA |
| 3 | 517 | 0.64 | 0.76 | 46 | empty |
| 4 | 142 | 0.63 | 0.86 | 24 | empty |
| 5 | 419 | 0.62 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 791 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 P42592
- Elsewhere: RCSB PDB 3W7X · PDBe 3W7X · UniProt P42592
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