Research workbench
The crystal structure of a thiol-disulfide isomerase from corynebacterium glutamicum to 2.2A
Analyse The crystal structure of a thiol-disulfide isomerase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LOR
- Type
- protein
- Length
- 610 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiol-disulfide isomerase and thioredoxins
- UniProt
- Q8NRX7
- Ligands
- CA, CL
- Pockets
- 5 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thiol-disulfide isomerase and thioredoxins | protein | 154 | 33% helix, 23% strand | Q8NRX7 |
| C | Thiol-disulfide isomerase and thioredoxins | protein | 152 | 34% helix, 23% strand | Q8NRX7 |
| D | Thiol-disulfide isomerase and thioredoxins | protein | 150 | 35% helix, 23% strand | Q8NRX7 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.38 | 0.81 | 17 | empty |
| 2 | 66 | 0.38 | 0.78 | 18 | empty |
| 3 | 59 | 0.37 | 0.79 | 17 | CL |
| 4 | 59 | 0.37 | 0.79 | 16 | empty |
| 5 | 53 | 0.36 | 0.79 | 10 | empty |
Interfaces
4 interfaces between chains.
- A–B · 709 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 700 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 686 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 668 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3LOR · The Crystal Structure of a Thiol-disulfide Isomerase from Corynebacterium glutamicum to… · 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 Q8NRX7
- Elsewhere: RCSB PDB 3LOR · PDBe 3LOR · UniProt Q8NRX7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.