MolNFT v1 · #78263 · protein
Transglutaminase 2 in complex with a novel inhibitor
3S3S · Protein-glutamine gamma-glutamyltransferase 2: “Transglutaminase 2 in complex with a novel inhibitor”. X-ray diffraction, 2 ligands (PHQ, SO4), 5 pockets (best druggability 0.62). MolNFT v1 #78263 on GenesisL1: 3D structure, binding…
- PDB
- 3S3S
- Type
- protein
- Length
- 624 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
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13) | protein | 620 | 19% helix, 41% 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.62 | 0.80 | 34 | empty |
| 2 | 90 | 0.46 | 0.80 | 21 | empty |
| 3 | 77 | 0.40 | 0.78 | 12 | empty |
| 4 | 52 | 0.28 | 0.75 | 17 | empty |
| 5 | 53 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 480 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 3S3S · 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 0.65
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 3S3S · PDBe 3S3S · UniProt P21980
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