MolNFT v1 · #120578 · protein
Structure of glutamyl-tRNA synthetase (XOO1504) from xanthomonas oryzae pv. oryzae
5H4V · Glutamate--tRNA ligase: “Structure of glutamyl-tRNA synthetase (XOO1504) from xanthomonas oryzae pv. oryzae”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #120578 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5H4V
- Type
- protein
- Length
- 2,775 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate--tRNA ligase
- EC
- 6.1.1.17
- UniProt
- Q5H2R3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Glutamate--tRNA ligase (EC 6.1.1.17) | protein | 465 | 46% helix, 12% strand | Q5H2R3 |
| B | Glutamate--tRNA ligase (EC 6.1.1.17) | protein | 460 | 49% helix, 12% strand | Q5H2R3 |
| C | Glutamate--tRNA ligase (EC 6.1.1.17) | protein | 455 | 47% helix, 11% strand | Q5H2R3 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.81 | 0.84 | 95 | empty |
| 2 | 1006 | 0.81 | 0.82 | 114 | empty |
| 3 | 807 | 0.80 | 0.83 | 92 | empty |
| 4 | 938 | 0.79 | 0.81 | 111 | empty |
| 5 | 634 | 0.77 | 0.83 | 79 | empty |
Interfaces
12 interfaces between chains.
- C–F · 945 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 893 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 887 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 880 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 879 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5H4V · Structure of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas oryzae pv. oryzae · the same entry in another collection · chain F against F, TM-score 1.00
- Q5H2R3 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase (Q5H2R3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q5H2R3
- Elsewhere: RCSB PDB 5H4V · PDBe 5H4V · UniProt Q5H2R3
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