Research workbench
Catalytic domain from trimeric dihydrolipoamide succinyltransferase
Analyse Catalytic domain from trimeric dihydrolipoamide succinyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C4T
- Type
- protein
- Length
- 667 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (dihydrolipoamide succinyltransferase)
- EC
- 2.3.1.61
- UniProt
- P07016
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (dihydrolipoamide succinyltransferase) (EC 2.3.1.61) | protein | 226 | 37% helix, 28% strand | P07016 |
| B | Protein (dihydrolipoamide succinyltransferase) (EC 2.3.1.61) | protein | 217 | 40% helix, 26% strand | P07016 |
| C | Protein (dihydrolipoamide succinyltransferase) (EC 2.3.1.61) | protein | 224 | 35% helix, 27% strand | P07016 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.79 | 0.97 | 20 | empty |
| 2 | 766 | 0.75 | 0.80 | 76 | SO4 |
| 3 | 577 | 0.71 | 0.80 | 64 | SO4 |
| 4 | 403 | 0.69 | 0.81 | 46 | SO4 |
| 5 | 60 | 0.66 | 0.94 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1507 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1360 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1275 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1C4T · Catalytic domain from trimeric dihydrolipoamide succinyltransferase · 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 P07016
- Elsewhere: RCSB PDB 1C4T · PDBe 1C4T · UniProt P07016
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