Research workbench
Crystal structure of a putative ASP/GLU racemase from yersinia pestis
Analyse Crystal structure of a putative ASP/GLU racemase from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OJC
- Type
- protein
- Length
- 920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ASPARTATE/GLUTAMATE racemase
- UniProt
- Q74SZ5
- Ligands
- CA
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative ASPARTATE/GLUTAMATE racemase | protein | 230 | 60% helix, 13% strand | Q74SZ5 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- HEZ · Hexane-1,6-diol · additive · 20 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.82 | 0.83 | 110 | CA |
| 2 | 692 | 0.79 | 0.83 | 73 | empty |
| 3 | 593 | 0.72 | 0.79 | 64 | CA, HEZ |
| 4 | 85 | 0.43 | 0.80 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1464 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1425 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 652 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 405 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 314 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3OJC · Crystal structure of a putative Asp/Glu Racemase from Yersinia pestis · 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 Q74SZ5
- Elsewhere: RCSB PDB 3OJC · PDBe 3OJC · UniProt Q74SZ5
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