Research workbench
The crystal structure of thioredoxin protein from geobacter metallireducens
Analyse The crystal structure of thioredoxin protein from geobacter metallireducens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KCM
- Type
- protein
- Length
- 840 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin family protein
- UniProt
- Q39SU7
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin family protein | protein | 139 | 33% helix, 27% strand | Q39SU7 |
| B | Thioredoxin family protein | protein | 141 | 33% helix, 27% strand | Q39SU7 |
| C | Thioredoxin family protein | protein | 139 | 34% helix, 27% strand | Q39SU7 |
| D | Thioredoxin family protein | protein | 142 | 33% helix, 26% strand | Q39SU7 |
| E | Thioredoxin family protein | protein | 141 | 35% helix, 25% strand | Q39SU7 |
| F | Thioredoxin family protein | protein | 138 | 32% helix, 28% strand | Q39SU7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.63 | 0.86 | 17 | empty |
| 2 | 301 | 0.60 | 0.78 | 45 | empty |
| 3 | 125 | 0.60 | 0.85 | 19 | empty |
| 4 | 129 | 0.59 | 0.85 | 22 | empty |
| 5 | 400 | 0.58 | 0.75 | 47 | empty |
Interfaces
5 interfaces between chains.
- A–D · 459 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 446 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 433 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 426 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified, 6 disulfide (engineered, disulfide).
Compared structures
- 3KCM · The crystal structure of thioredoxin protein from Geobacter metallireducens · 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 Q39SU7
- Elsewhere: RCSB PDB 3KCM · PDBe 3KCM · UniProt Q39SU7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.