MolNFT v1 · #113027 · protein
The crystal structure of the GST-like domains complex of eprs-AIMP2
5A34 · Bifunctional GLUTAMATE/PROLINE--tRNA ligase: “The crystal structure of the GST-like domains complex of eprs-AIMP2”. X-ray diffraction, 20 pockets (best druggability 0.67). MolNFT v1 #113027 on GenesisL1: 3D structure, binding sites…
- PDB
- 5A34
- Type
- protein
- Length
- 1,467 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional GLUTAMATE/PROLINE--tRNA ligase; Aminoacyl tRNA synthase complex-interacting…
- EC
- 6.1.1.15, 6.1.1.17
- UniProt
- P07814, Q13155
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 8 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.15, 6.1.1.17) | protein | 168 | 54% helix, 10% strand | P07814 |
| B | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 204 | 46% helix, 13% strand | Q13155 |
| C | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.15, 6.1.1.17) | protein | 170 | 54% helix, 8% strand | P07814 |
| D | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 196 | 47% helix, 14% strand | Q13155 |
| E | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.15, 6.1.1.17) | protein | 167 | 57% helix, 10% strand | P07814 |
| F | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 201 | 44% helix, 13% strand | Q13155 |
| G | Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.15, 6.1.1.17) | protein | 168 | 54% helix, 12% strand | P07814 |
| H | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 193 | 45% helix, 14% strand | Q13155 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.67 | 0.82 | 35 | empty |
| 2 | 383 | 0.63 | 0.78 | 48 | empty |
| 3 | 228 | 0.63 | 0.82 | 32 | empty |
| 4 | 188 | 0.61 | 0.83 | 32 | empty |
| 5 | 244 | 0.60 | 0.80 | 31 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1235 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1197 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1152 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1139 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 541 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5A34 · The crystal structure of the GST-like domains complex of EPRS-AIMP2 · the same entry in another collection · chain H against H, TM-score 1.00
- P07814 · AlphaFold monomer V2.0 prediction for bifunctional GLUTAMATE/PROLINE --tRNA ligase… · a predicted model of the same protein · chain E against A, TM-score 0.98
- Q13155 · AlphaFold monomer V2.0 prediction for aminoacyl tRNA synthase complex-interacting… · a predicted model of the same protein · chain D 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 P07814
- Every structure of UniProt Q13155
- Elsewhere: RCSB PDB 5A34 · PDBe 5A34 · UniProt P07814 · UniProt Q13155
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