Research workbench
Crystal structure of E. COLI GRX2 in complex with gsh at 1.45 a resolution
Analyse Crystal structure of E. COLI GRX2 in complex with gsh at 1.45 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DKP
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaredoxin
- UniProt
- C3TEC2
- Ligands
- GSH
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutaredoxin | protein | 215 | 56% helix, 7% strand | C3TEC2 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, C, B, D
- FLC · Citrate anion · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.87 | 0.88 | 92 | GSH |
| 2 | 358 | 0.60 | 0.77 | 47 | empty |
| 3 | 328 | 0.57 | 0.76 | 29 | empty |
| 4 | 235 | 0.55 | 0.77 | 28 | GSH |
| 5 | 325 | 0.54 | 0.75 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1032 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 350 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 258 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7DKP · Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A resolution · 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 C3TEC2
- Elsewhere: RCSB PDB 7DKP · PDBe 7DKP · UniProt C3TEC2
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