Research workbench
Transglutaminase 2 in complex with a novel inhibitor
Analyse Transglutaminase 2 in complex with a novel inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S3P
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-glutamine gamma-glutamyltransferase 2; Peptide inhibitor
- EC
- 2.3.2.13
- UniProt
- P21980
- Ligands
- PHQ, SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13) | protein | 611 | 18% helix, 40% strand | P21980 |
| B | Peptide inhibitor | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.63 | 0.78 | 45 | empty |
| 2 | 101 | 0.49 | 0.81 | 22 | empty |
| 3 | 115 | 0.44 | 0.77 | 29 | empty |
| 4 | 81 | 0.34 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 3S3P · Transglutaminase 2 in complex with a novel inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P21980 · AlphaFold monomer V2.0 prediction for protein-glutamine gamma- glutamyltransferase 2… · a predicted model of the same protein · chain A against A, TM-score 0.66
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 P21980
- Elsewhere: RCSB PDB 3S3P · PDBe 3S3P · UniProt P21980
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