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Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from deinococcus radiodurans
Analyse Structural basis for catalytic racemization and substrate specificity of an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XS2
- Type
- protein
- Length
- 1,440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylamino acid racemase
- UniProt
- Q9RYA6
- Ligands
- MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-acylamino acid racemase | protein | 360 | 36% helix, 23% strand | Q9RYA6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.79 | 0.83 | 80 | empty |
| 2 | 702 | 0.78 | 0.83 | 83 | empty |
| 3 | 355 | 0.73 | 0.85 | 36 | empty |
| 4 | 338 | 0.59 | 0.77 | 36 | MG |
| 5 | 345 | 0.58 | 0.77 | 41 | MG |
Interfaces
3 interfaces between chains.
- A–C · 1270 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1246 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 961 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1XS2 · Structural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino… · 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 Q9RYA6
- Elsewhere: RCSB PDB 1XS2 · PDBe 1XS2 · UniProt Q9RYA6
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