MolNFT v1 · #104144 · protein
Crystal structure of a glutamate 5-kinase from burkholderia thailandensis
4Q1T: “Crystal structure of a glutamate 5-kinase from burkholderia thailandensis”. X-ray diffraction, 13 pockets (best druggability 0.87). MolNFT v1 #104144 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Q1T
- Type
- protein
- Length
- 1,375 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate 5-kinase
- EC
- 2.7.2.11
- UniProt
- Q2SZF9
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate 5-kinase (EC 2.7.2.11) | protein | 340 | 43% helix, 23% strand | Q2SZF9 |
| B | Glutamate 5-kinase (EC 2.7.2.11) | protein | 353 | 44% helix, 23% strand | Q2SZF9 |
| C | Glutamate 5-kinase (EC 2.7.2.11) | protein | 351 | 44% helix, 23% strand | Q2SZF9 |
| D | Glutamate 5-kinase (EC 2.7.2.11) | protein | 331 | 46% helix, 22% strand | Q2SZF9 |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.87 | 0.89 | 144 | empty |
| 2 | 731 | 0.80 | 0.84 | 92 | empty |
| 3 | 620 | 0.79 | 0.85 | 98 | empty |
| 4 | 98 | 0.71 | 0.94 | 25 | empty |
| 5 | 135 | 0.63 | 0.86 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2168 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2061 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 850 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 346 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Q1T · Crystal structure of a glutamate 5-kinase from Burkholderia thailandensis · the same entry in another collection · chain D against D, TM-score 1.00
- Q2SZF9 · AlphaFold monomer V2.0 prediction for glutamate 5-kinase (Q2SZF9) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q2SZF9
- Elsewhere: RCSB PDB 4Q1T · PDBe 4Q1T · UniProt Q2SZF9
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