MolNFT v1 · #166220 · protein
Crystal structure of cysteine-tRNA ligase from elizabethkingia sp.
6UJD · Cysteine--tRNA ligase: “Crystal structure of cysteine-tRNA ligase from elizabethkingia sp.”. X-ray diffraction, 3 ligands (ZN, CL, PO4), 4 pockets (best druggability 0.63). MolNFT v1 #166220 on GenesisL1: 3D structure, binding sites…
- PDB
- 6UJD
- Type
- protein
- Length
- 406 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine--tRNA ligase
- EC
- 6.1.1.16
- UniProt
- A0A1T3F4R2
- Ligands
- ZN, CL, PO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine--tRNA ligase (EC 6.1.1.16) | protein | 406 | 44% helix, 17% strand | A0A1T3F4R2 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.63 | 0.80 | 37 | CL |
| 2 | 88 | 0.36 | 0.75 | 21 | CL |
| 3 | 62 | 0.33 | 0.75 | 13 | empty |
| 4 | 56 | 0.29 | 0.75 | 12 | empty |
Compared structures
- 6UJD · Crystal structure of Cysteine-tRNA ligase from Elizabethkingia sp. · the same entry in another collection · chain A against A, 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 A0A1T3F4R2
- Elsewhere: RCSB PDB 6UJD · PDBe 6UJD · UniProt A0A1T3F4R2
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