Research workbench
Prx D (type II) from populus tremula
Analyse Prx D (type II) from populus tremula in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TP9
- Type
- protein
- Length
- 646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin
- UniProt
- Q8S3L0
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Peroxiredoxin | protein | 162 | 27% helix, 30% strand | Q8S3L0 |
| D | Peroxiredoxin | protein | 160 | 28% helix, 30% strand | Q8S3L0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.77 | 0.81 | 79 | empty |
| 2 | 146 | 0.46 | 0.76 | 22 | empty |
| 3 | 159 | 0.45 | 0.76 | 19 | empty |
| 4 | 153 | 0.44 | 0.75 | 20 | empty |
| 5 | 122 | 0.42 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 348 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 248 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 234 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 151 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 116 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1TP9 · PRX D (type II) from Populus tremula · 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 Q8S3L0
- Elsewhere: RCSB PDB 1TP9 · PDBe 1TP9 · UniProt Q8S3L0
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