Research workbench
Crystal structure of the AIMP3-mrs N-terminal domain complex with I3C
Analyse Crystal structure of the AIMP3-mrs N-terminal domain complex with I3C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BVX
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine--tRNA ligase, cytoplasmic; Eukaryotic translation elongation factor 1 epsilon-1
- EC
- 6.1.1.10
- UniProt
- P56192, O43324
- Ligands
- I3C
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine--tRNA ligase, cytoplasmic (EC 6.1.1.10) | protein | 203 | 57% helix, 6% strand | P56192 |
| B | Eukaryotic translation elongation factor 1 epsilon-1 | protein | 170 | 57% helix, 8% strand | O43324 |
Ligands and binding sites
- I3C · 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.69 | 0.97 | 16 | empty |
| 2 | 584 | 0.69 | 0.78 | 50 | empty |
| 3 | 296 | 0.61 | 0.79 | 40 | empty |
| 4 | 75 | 0.39 | 0.78 | 14 | I3C |
Interfaces
1 interface between chains.
- A–B · 1344 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4BVX · Crystal structure of the AIMP3-MRS N-terminal domain complex with I3C · the same entry in another collection · chain A against A, TM-score 1.00
- P56192 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase, cytoplasmic (P56192) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O43324 · AlphaFold monomer V2.0 prediction for eukaryotic translation elongation factor 1… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P56192
- Every structure of UniProt O43324
- Elsewhere: RCSB PDB 4BVX · PDBe 4BVX · UniProt P56192 · UniProt O43324
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