MolNFT v1 · #13378 · protein
Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions change structure for activation
1L9M · Protein-glutamine glutamyltransferase E3: “Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions change structure…”. X-ray diffraction, 3 ligands (CA, BR, CL), 11 pockets (best druggability…
- PDB
- 1L9M
- Type
- protein
- Length
- 1,356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-glutamine glutamyltransferase E3
- EC
- 2.3.2.13
- UniProt
- Q08188
- Ligands
- CA, BR, CL
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-glutamine glutamyltransferase E3 (EC 2.3.2.13) | protein | 675 | 17% helix, 42% strand | Q08188 |
| B | Protein-glutamine glutamyltransferase E3 (EC 2.3.2.13) | protein | 681 | 17% helix, 42% strand | Q08188 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.67 | 0.83 | 33 | empty |
| 2 | 263 | 0.65 | 0.82 | 32 | empty |
| 3 | 317 | 0.62 | 0.79 | 37 | empty |
| 4 | 265 | 0.61 | 0.80 | 34 | empty |
| 5 | 224 | 0.55 | 0.78 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 803 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1L9M · Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08188 · AlphaFold monomer V2.0 prediction for protein-glutamine gamma- glutamyltransferase E… · a predicted model of the same protein · 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 Q08188
- Elsewhere: RCSB PDB 1L9M · PDBe 1L9M · UniProt Q08188
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