Research workbench
Crystal structure of glutamate racemase from listeria monocytogenes in complex with succinic acid
Analyse Crystal structure of glutamate racemase from listeria monocytogenes in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IST
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q8Y7N7
- Ligands
- CL
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase (EC 5.1.1.3) | protein | 268 | 49% helix, 16% strand | Q8Y7N7 |
| B | Glutamate racemase (EC 5.1.1.3) | protein | 266 | 49% helix, 17% strand | Q8Y7N7 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.55 | 0.82 | 28 | SIN |
| 2 | 132 | 0.50 | 0.80 | 24 | empty |
| 3 | 244 | 0.49 | 0.74 | 26 | empty |
| 4 | 178 | 0.48 | 0.76 | 24 | CL |
| 5 | 54 | 0.38 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1439 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3IST · Crystal structure of glutamate racemase from Listeria monocytogenes in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8Y7N7 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q8Y7N7) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8Y7N7
- Elsewhere: RCSB PDB 3IST · PDBe 3IST · UniProt Q8Y7N7
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