Research workbench
Crystal structure of glutamate racemase from francisella tularensis subsp. tularensis schu S4 in complex with D-glutamate.
Analyse Crystal structure of glutamate racemase from francisella tularensis subsp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OUT
- Type
- protein
- Length
- 791 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q5NFN6
- Ligands
- DGL
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase (EC 5.1.1.3) | protein | 263 | 45% helix, 17% strand | Q5NFN6 |
| B, C | Glutamate racemase (EC 5.1.1.3) | protein | 264 | 45% helix, 17% strand | Q5NFN6 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.84 | 0.84 | 112 | DGL |
| 2 | 120 | 0.61 | 0.87 | 25 | empty |
| 3 | 59 | 0.60 | 0.91 | 24 | DGL |
| 4 | 246 | 0.60 | 0.80 | 45 | empty |
| 5 | 74 | 0.31 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1256 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 772 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 600 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3OUT · Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis… · 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 Q5NFN6
- Elsewhere: RCSB PDB 3OUT · PDBe 3OUT · UniProt Q5NFN6
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