MolNFT v1 · #67719 · protein
Crystal structure of glutamate racemase from listeria monocytogenes in complex with succinic acid
3IST: “Crystal structure of glutamate racemase from listeria monocytogenes in complex with succinic acid”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.55). MolNFT v1 #67719 on GenesisL1: 3D structure, binding sites and…
- 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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