Research workbench
Crystal structure of pyrococcus horikoshii OT3 aspartate racemase complex with citric acid
Analyse Crystal structure of pyrococcus horikoshii OT3 aspartate racemase complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DX7
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate racemase
- EC
- 5.1.1.13
- UniProt
- O58403
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartate racemase (EC 5.1.1.13) | protein | 228 | 57% helix, 12% strand | O58403 |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.66 | 0.80 | 41 | empty |
| 2 | 72 | 0.33 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1474 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2DX7 · Crystal structure of Pyrococcus horikoshii OT3 aspartate racemase complex with citric acid · the same entry in another collection · chain A against A, TM-score 1.00
- O58403 · AlphaFold monomer V2.0 prediction for aspartate racemase (O58403) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O58403
- Elsewhere: RCSB PDB 2DX7 · PDBe 2DX7 · UniProt O58403
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