Research workbench
X-ray crystal structure of a tyrosine aminomutase mutant construct with bound ligand
Analyse X-ray crystal structure of a tyrosine aminomutase mutant construct with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KDZ
- Type
- protein
- Length
- 1,054 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine ammonia-lyase
- EC
- 4.3.1.3
- UniProt
- Q8GMG0
- Ligands
- TYR
- Pockets
- 11 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histidine ammonia-lyase (EC 4.3.1.3) | protein | 527 | 57% helix, 6% strand | Q8GMG0 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.53 | 0.83 | 27 | TYR |
| 2 | 103 | 0.51 | 0.82 | 26 | TYR |
| 3 | 53 | 0.47 | 0.86 | 25 | empty |
| 4 | 120 | 0.44 | 0.77 | 23 | empty |
| 5 | 99 | 0.43 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 4878 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 B against A, TM-score 1.00
- 3KDZ · X-ray crystal structure of a tyrosine aminomutase mutant construct with bound ligand · 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 3KDZ · PDBe 3KDZ · UniProt Q8GMG0
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