Research workbench
Crystal structure of the pirin family protein redox-sensitive bicupin yhak from yersinia pestis
Analyse Crystal structure of the pirin family protein redox-sensitive bicupin yhak from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TE5
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pirin family protein yhak
- UniProt
- A0A2U2H063
- Ligands
- MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pirin family protein yhak | protein | 284 | 13% helix, 53% strand | A0A2U2H063 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.72 | 0.81 | 48 | MG |
| 2 | 344 | 0.63 | 0.79 | 48 | empty |
| 3 | 131 | 0.53 | 0.81 | 19 | empty |
| 4 | 142 | 0.42 | 0.75 | 19 | empty |
| 5 | 52 | 0.27 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 7TE5 · Crystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK from Yersinia… · 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 A0A2U2H063
- Elsewhere: RCSB PDB 7TE5 · PDBe 7TE5 · UniProt A0A2U2H063
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