Research workbench
Crystal structure of thioredoxin 2 from yersinia pestis
Analyse Crystal structure of thioredoxin 2 from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P2A
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative thioredoxin-like protein
- UniProt
- Q7CK81
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative thioredoxin-like protein | protein | 145 | 27% helix, 26% strand | Q7CK81 |
| B | Putative thioredoxin-like protein | protein | 144 | 27% helix, 28% strand | Q7CK81 |
| C | Putative thioredoxin-like protein | protein | 141 | 27% helix, 25% strand | Q7CK81 |
| D | Putative thioredoxin-like protein | protein | 142 | 27% helix, 26% strand | Q7CK81 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.70 | 0.78 | 55 | empty |
| 2 | 697 | 0.69 | 0.77 | 75 | empty |
| 3 | 161 | 0.45 | 0.76 | 22 | empty |
| 4 | 55 | 0.26 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–D · 685 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 482 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 428 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 245 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 95 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 3P2A · Crystal Structure of Thioredoxin 2 from Yersinia pestis · 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 Q7CK81
- Elsewhere: RCSB PDB 3P2A · PDBe 3P2A · UniProt Q7CK81
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