Research workbench
Crystal structure of human lysrs: P38/AIMP2 complex I
Analyse Crystal structure of human lysrs: P38/AIMP2 complex I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DPG
- Type
- protein
- Length
- 4,148 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase; Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
- EC
- 6.1.1.6
- UniProt
- Q15046, Q13155
- Ligands
- LYS, APC, ALA, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 501 | 37% helix, 25% strand | Q15046 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 506 | 36% helix, 25% strand | Q15046 |
| D, F, H | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 505 | 36% helix, 25% strand | Q15046 |
| E | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 500 | 37% helix, 25% strand | Q15046 |
| G | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 501 | 37% helix, 25% strand | Q15046 |
| I, J, K, L | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 31 | 0% helix, 0% strand | Q13155 |
Ligands and binding sites
- LYS · Lysine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ALA · Alanine · ligand · chains H
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, K, G, H, I, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 174 | 0.82 | 0.97 | 47 | empty |
| 2 | 165 | 0.81 | 0.97 | 44 | empty |
| 3 | 139 | 0.81 | 0.98 | 37 | empty |
| 4 | 1178 | 0.81 | 0.82 | 99 | empty |
| 5 | 112 | 0.78 | 0.98 | 28 | empty |
Interfaces
20 interfaces between chains.
- G–H · 4378 Ų buried · 73 hydrogen bonds · protein-protein
- E–F · 4365 Ų buried · 74 hydrogen bonds · protein-protein
- A–B · 4362 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 4347 Ų buried · 69 hydrogen bonds · protein-protein
- E–L · 1297 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4DPG · Crystal Structure of Human LysRS: P38/AIMP2 Complex I · the same entry in another collection · chain L against L, TM-score 1.00
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 Q15046
- Every structure of UniProt Q13155
- Elsewhere: RCSB PDB 4DPG · PDBe 4DPG · UniProt Q15046 · UniProt Q13155
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