Research workbench
Probable N-succinyldiaminopimelate aminotransferase (TTHA0342) from thermus thermophilus HB8
Analyse Probable N-succinyldiaminopimelate aminotransferase (TTHA0342) from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DOU
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable N-succinyldiaminopimelate aminotransferase
- EC
- 2.-.-.-
- UniProt
- Q5SLF1
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable N-succinyldiaminopimelate aminotransferase (EC 2.-.-.-) | protein | 372 | 49% helix, 16% strand | Q5SLF1 |
| B | Probable N-succinyldiaminopimelate aminotransferase (EC 2.-.-.-) | protein | 368 | 48% helix, 16% strand | Q5SLF1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.74 | 0.81 | 68 | SO4 |
| 2 | 732 | 0.74 | 0.79 | 54 | SO4, EPE |
| 3 | 124 | 0.48 | 0.79 | 28 | empty |
| 4 | 77 | 0.39 | 0.78 | 22 | empty |
| 5 | 59 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1687 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DOU · probable N-succinyldiaminopimelate aminotransferase (TTHA0342) from Thermus thermophilus… · 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 Q5SLF1
- Elsewhere: RCSB PDB 2DOU · PDBe 2DOU · UniProt Q5SLF1
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