MolNFT v1 · #24963 · protein
Crystal structure of the escherichia COLI tyrosyl-tRNA synthetase complexed with tyr-ams
1VBM: “Crystal structure of the escherichia COLI tyrosyl-tRNA synthetase complexed with tyr-ams”. X-ray diffraction, 2 ligands (YSA, SO4), 4 pockets (best druggability 0.70). MolNFT v1 #24963 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1VBM
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-tRNA synthetase
- EC
- 6.1.1.1
- UniProt
- P00951
- Ligands
- YSA, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 318 | 55% helix, 10% strand | P00951 |
Ligands and binding sites
- YSA · 5'-O-[N-(L-tyrosyl)sulfamoyl]adenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.70 | 0.82 | 42 | SO4, YSA |
| 2 | 385 | 0.70 | 0.82 | 41 | SO4, YSA |
| 3 | 90 | 0.38 | 0.76 | 15 | empty |
| 4 | 75 | 0.37 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1481 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1VBM · Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS · 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 P00951
- Elsewhere: RCSB PDB 1VBM · PDBe 1VBM · UniProt P00951
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