MolNFT v1 · #146570 · protein
Crystal structure of glutamate racemase from thermus thermophilus in complex with beta-chloro-D-alanine
6DLI: “Crystal structure of glutamate racemase from thermus thermophilus in complex with beta-chloro-D-alanine”. X-ray diffraction, 1 ligand (C2N), 7 pockets (best druggability 0.82). MolNFT v1 #146570 on GenesisL1: 3D structure, binding…
- PDB
- 6DLI
- 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
- C2N
- Pockets
- 7 · 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
- C2N · 3-chloro-D-alanine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.82 | 0.83 | 64 | empty |
| 2 | 996 | 0.82 | 0.83 | 88 | C2N |
| 3 | 1002 | 0.82 | 0.83 | 91 | C2N |
| 4 | 102 | 0.43 | 0.77 | 21 | empty |
| 5 | 96 | 0.40 | 0.77 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 836 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 819 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 724 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 711 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DLI · Crystal structure of glutamate racemase from Thermus thermophilus in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q5SHT7 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q5SHT7) · a predicted model of the same protein · chain B 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 6DLI · PDBe 6DLI · UniProt Q5SHT7
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