Research workbench
Crystal structure of putative glycerate kinase 2 from salmonella typhimurium LT2
Analyse Crystal structure of putative glycerate kinase 2 from salmonella typhimurium LT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CWC
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycerate kinase 2
- UniProt
- Q8ZME0
- Ligands
- CL
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glycerate kinase 2 | protein | 369 | 41% helix, 19% strand | Q8ZME0 |
| B | Putative glycerate kinase 2 | protein | 374 | 40% helix, 19% strand | Q8ZME0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.60 | 0.76 | 43 | empty |
| 2 | 337 | 0.59 | 0.77 | 34 | empty |
| 3 | 216 | 0.51 | 0.76 | 26 | empty |
| 4 | 98 | 0.38 | 0.76 | 23 | empty |
| 5 | 99 | 0.36 | 0.75 | 23 | EDO |
Interfaces
1 interface between chains.
- A–B · 856 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3CWC · Crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2 · 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 Q8ZME0
- Elsewhere: RCSB PDB 3CWC · PDBe 3CWC · UniProt Q8ZME0
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