Research workbench
Crystal structure of a broad specificity amino acid racemase (bar) within internal aldimine linkage
Analyse Crystal structure of a broad specificity amino acid racemase (bar) within… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DYJ
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Broad specificity amino acid racemase
- EC
- 5.1.1.10
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Broad specificity amino acid racemase (EC 5.1.1.10) | protein | 384 | 36% helix, 26% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.71 | 0.96 | 22 | empty |
| 2 | 296 | 0.64 | 0.81 | 46 | empty |
| 3 | 234 | 0.64 | 0.83 | 37 | GOL |
| 4 | 71 | 0.35 | 0.76 | 17 | empty |
| 5 | 51 | 0.32 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3536 Ų buried · 63 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, cofactor).
Compared structures
- 4DYJ · Crystal structure of a broad specificity amino acid racemase (Bar) within internal… · 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 4DYJ · PDBe 4DYJ
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