Research workbench
Crystal structure of sgtam bound to mechanism based inhibitor
Analyse Crystal structure of sgtam bound to mechanism based inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QVE
- Type
- protein
- Length
- 1,052 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine aminomutase
- EC
- 5.4.3.6
- UniProt
- Q8GMG0
- Ligands
- 247
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine aminomutase (EC 5.4.3.6) | protein | 526 | 57% helix, 7% strand | Q8GMG0 |
Ligands and binding sites
- 247 · (3R)-3-amino-2,2-difluoro-3-(4-hydroxyphenyl)propanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.56 | 0.82 | 25 | empty |
| 2 | 197 | 0.53 | 0.78 | 37 | 247 |
| 3 | 162 | 0.51 | 0.78 | 38 | 247 |
| 4 | 100 | 0.40 | 0.77 | 24 | empty |
| 5 | 78 | 0.39 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 4913 Ų buried · 89 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- Q8GMG0 · AlphaFold monomer V2.0 prediction for mio-dependent tyrosine 2,3-aminomutase (Q8GMG0) · a predicted model of the same protein · chain A against A, TM-score 1.00
- 2QVE · Crystal Structure of SgTAM bound to mechanism based inhibitor · 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 Q8GMG0
- Elsewhere: RCSB PDB 2QVE · PDBe 2QVE · UniProt Q8GMG0
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