Research workbench
Crystal structure of L-ASPARTATE/GLUTAMATE specific racemase in complex with L-glutamate
Analyse Crystal structure of L-ASPARTATE/GLUTAMATE specific racemase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ELM
- Type
- protein
- Length
- 940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASP/GLU_RACEMASE family protein
- EC
- 5.1.1.13
- UniProt
- C3SWD2
- Ligands
- GLU, NO3
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ASP/GLU_RACEMASE family protein (EC 5.1.1.13) | protein | 235 | 59% helix, 12% strand | C3SWD2 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains B, C, D
- NO3 · Nitrate ion · ion · chains D
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.66 | 0.79 | 48 | empty |
| 2 | 210 | 0.46 | 0.74 | 33 | empty |
| 3 | 109 | 0.41 | 0.76 | 20 | empty |
| 4 | 104 | 0.41 | 0.77 | 20 | empty |
| 5 | 106 | 0.38 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1562 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1451 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 185 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 72 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ELM · Crystal structure of L-aspartate/glutamate specific racemase in complex with L-glutamate · 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 C3SWD2
- Elsewhere: RCSB PDB 5ELM · PDBe 5ELM · UniProt C3SWD2
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