Research workbench
Crystal structure of DUF1341 representative, from yersinia enterocolitica subsp. enterocolitica 8081
Analyse Crystal structure of DUF1341 representative, from yersinia enterocolitica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LM7
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 4-hydroxy-2-oxoglutarate aldolase / 2- dehydro-3-deoxyphosphogluconate aldolase
- UniProt
- A1JRF3
- Ligands
- K, BR
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 4-hydroxy-2-oxoglutarate aldolase / 2- dehydro-3-deoxyphosphogluconate aldolase | protein | 249 | 43% helix, 18% strand | A1JRF3 |
| B | Putative 4-hydroxy-2-oxoglutarate aldolase / 2- dehydro-3-deoxyphosphogluconate aldolase | protein | 246 | 43% helix, 18% strand | A1JRF3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.56 | 0.77 | 31 | empty |
| 2 | 199 | 0.53 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 406 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3LM7 · Crystal Structure of DUF1341 representative, from Yersinia enterocolitica subsp.… · 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 A1JRF3
- Elsewhere: RCSB PDB 3LM7 · PDBe 3LM7 · UniProt A1JRF3
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