Research workbench
Crystal structure of cysteinyl-tRNA synthetase binary complex with trnacys
Analyse Crystal structure of cysteinyl-tRNA synthetase binary complex with trnacys in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U0B
- Type
- protein + RNA
- Length
- 535 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteinyl-tRNA synthetase; Cysteinyl tRNA
- EC
- 6.1.1.16
- UniProt
- P21888
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteinyl-tRNA synthetase (EC 6.1.1.16) | rna | 74 | — | — |
| B | Cysteinyl tRNA | protein | 461 | 45% helix, 16% strand | P21888 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.78 | 0.81 | 66 | empty |
| 2 | 89 | 0.75 | 0.97 | 16 | empty |
| 3 | 972 | 0.74 | 0.78 | 64 | empty |
| 4 | 339 | 0.68 | 0.82 | 46 | empty |
| 5 | 100 | 0.52 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2347 Ų buried · 47 hydrogen bonds · protein-nucleic
Compared structures
- 1U0B · Crystal structure of cysteinyl-tRNA synthetase binary complex with tRNACys · the same entry in another collection · chain A against A, TM-score 1.00
- P21888 · AlphaFold monomer V2.0 prediction for cysteine--tRNA ligase (P21888) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P21888
- Elsewhere: RCSB PDB 1U0B · PDBe 1U0B · UniProt P21888
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