MolNFT v1 · #56872 · protein
Crystal structure of human glycyl-tRNA synthetase (glyrs) in complex with ampcpp
2ZT6: “Crystal structure of human glycyl-tRNA synthetase (glyrs) in complex with ampcpp”. X-ray diffraction, 1 ligand (APC), 6 pockets (best druggability 0.81). MolNFT v1 #56872 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZT6
- Type
- protein
- Length
- 530 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycyl-tRNA synthetase
- EC
- 6.1.1.14
- UniProt
- P41250
- Ligands
- APC
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycyl-tRNA synthetase (EC 6.1.1.14) | protein | 530 | 38% helix, 24% strand | P41250 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.81 | 0.82 | 83 | APC |
| 2 | 81 | 0.47 | 0.81 | 18 | empty |
| 3 | 52 | 0.40 | 0.82 | 16 | empty |
| 4 | 100 | 0.38 | 0.75 | 26 | empty |
| 5 | 63 | 0.31 | 0.75 | 14 | empty |
Compared structures
- 2ZT6 · Crystal structure of human Glycyl-tRNA synthetase (GlyRS) in complex with AMPCPP · the same entry in another collection · chain A against A, TM-score 1.00
- P41250 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase (P41250) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P41250
- Elsewhere: RCSB PDB 2ZT6 · PDBe 2ZT6 · UniProt P41250
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