Research workbench
Crystal structure of E. COLI tyrosyl-tRNA synthetase in complex with TYRS7HMDDA
Analyse Crystal structure of E. COLI tyrosyl-tRNA synthetase in complex with TYRS7HMDDA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AP3
- Type
- protein
- Length
- 826 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine--tRNA ligase
- EC
- 6.1.1.1
- UniProt
- A0A140NBN7
- Ligands
- RRB, NA
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 413 | 53% helix, 14% strand | A0A140NBN7 |
| B | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 413 | 51% helix, 15% strand | A0A140NBN7 |
Ligands and binding sites
- RRB · [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.70 | 0.80 | 61 | RRB, NA |
| 2 | 396 | 0.68 | 0.81 | 40 | RRB, NA |
| 3 | 51 | 0.53 | 0.88 | 21 | empty |
| 4 | 89 | 0.38 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1710 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7AP3 · Crystal structure of E. coli tyrosyl-tRNA synthetase in complex with TyrS7HMDDA · 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 A0A140NBN7
- Elsewhere: RCSB PDB 7AP3 · PDBe 7AP3 · UniProt A0A140NBN7
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