Research workbench
Structure of TGPLP1 macpf domain
Analyse Structure of TGPLP1 macpf domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OUQ
- Type
- protein
- Length
- 1,656 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Perforin-like protein 1
- UniProt
- G3G7T1
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G | Perforin-like protein 1 | protein | 276 | 30% helix, 32% strand | G3G7T1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.70 | 0.79 | 45 | empty |
| 2 | 509 | 0.68 | 0.79 | 46 | empty |
| 3 | 477 | 0.68 | 0.79 | 52 | empty |
| 4 | 497 | 0.67 | 0.78 | 46 | empty |
| 5 | 436 | 0.66 | 0.79 | 53 | empty |
Interfaces
6 interfaces between chains.
- C–D · 814 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 788 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 780 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 777 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 773 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5OUQ · Structure of TgPLP1 MACPF domain · 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 G3G7T1
- Elsewhere: RCSB PDB 5OUQ · PDBe 5OUQ · UniProt G3G7T1
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