MolNFT v1 · #141208 · protein
Crystal structure of E.COLI lysu T146D mutant
5YZX · Lysine--tRNA ligase, heat inducible: “Crystal structure of E.COLI lysu T146D mutant”. X-ray diffraction, 2 ligands (B4P, CA), 16 pockets (best druggability 0.77). MolNFT v1 #141208 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YZX
- Type
- protein
- Length
- 1,453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase, heat inducible
- EC
- 6.1.1.6
- UniProt
- P0A8N5
- Ligands
- B4P, CA
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysine--tRNA ligase, heat inducible (EC 6.1.1.6) | protein | 484 | 37% helix, 27% strand | P0A8N5 |
| B | Lysine--tRNA ligase, heat inducible (EC 6.1.1.6) | protein | 485 | 38% helix, 27% strand | P0A8N5 |
Ligands and binding sites
- B4P · Bis(adenosine)-5'-tetraphosphate · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.77 | 0.84 | 55 | B4P, CA |
| 2 | 636 | 0.76 | 0.82 | 59 | B4P, CA |
| 3 | 601 | 0.75 | 0.82 | 58 | B4P, CA |
| 4 | 621 | 0.68 | 0.77 | 87 | empty |
| 5 | 211 | 0.66 | 0.84 | 26 | empty |
Interfaces
1 interface between chains.
- A–C · 4581 Ų buried · 81 hydrogen bonds · protein-protein
Compared structures
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 P0A8N5
- Elsewhere: RCSB PDB 5YZX · PDBe 5YZX · UniProt P0A8N5
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