MolNFT v1 · #103414 · protein
Crystal structure of krs complexed with inhibitor
4PG3 · Lysine--tRNA ligase: “Crystal structure of krs complexed with inhibitor”. X-ray diffraction, 2 ligands (LYS, KRS), 20 pockets (best druggability 0.84). MolNFT v1 #103414 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PG3
- Type
- protein
- Length
- 1,934 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- Q8IDJ8
- Ligands
- LYS, KRS
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 484 | 31% helix, 26% strand | Q8IDJ8 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 486 | 31% helix, 26% strand | Q8IDJ8 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 480 | 31% helix, 27% strand | Q8IDJ8 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- KRS · cladosporin · ligand · 4 copies · chains A, B, C, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.84 | 0.97 | 50 | empty |
| 2 | 198 | 0.82 | 0.96 | 51 | empty |
| 3 | 637 | 0.74 | 0.81 | 62 | LYS, KRS |
| 4 | 254 | 0.73 | 0.87 | 36 | empty |
| 5 | 534 | 0.73 | 0.81 | 60 | LYS, KRS |
Interfaces
3 interfaces between chains.
- A–B · 4615 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 4582 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 474 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4PG3 · Crystal structure of KRS complexed with inhibitor · the same entry in another collection · chain D against D, 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 Q8IDJ8
- Elsewhere: RCSB PDB 4PG3 · PDBe 4PG3 · UniProt Q8IDJ8
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