Research workbench
Crystal structure of glutamate racemase from thermus thermophilus in complex with D-glutamate
Analyse Crystal structure of glutamate racemase from thermus thermophilus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W16
- Type
- protein
- Length
- 1,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q5SHT7
- Ligands
- DGL, NO3, CL
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate racemase (EC 5.1.1.3) | protein | 256 | 43% helix, 17% strand | Q5SHT7 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 16 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.82 | 0.84 | 90 | DGL, NO3, CL |
| 2 | 894 | 0.82 | 0.84 | 88 | DGL, NO3, CL |
| 3 | 1059 | 0.82 | 0.83 | 58 | NO3, CL |
| 4 | 86 | 0.42 | 0.79 | 24 | empty |
| 5 | 99 | 0.42 | 0.77 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 841 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 816 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 698 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 697 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5W16 · Crystal structure of glutamate racemase from Thermus thermophilus in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q5SHT7 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q5SHT7) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q5SHT7
- Elsewhere: RCSB PDB 5W16 · PDBe 5W16 · UniProt Q5SHT7
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