Research workbench
Complex of tetrahydrodipicolinate N-succinyltransferase with 2- aminopimelate and coenzyme a
Analyse Complex of tetrahydrodipicolinate N-succinyltransferase with 2- aminopimelate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2TDT
- Type
- protein
- Length
- 274 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahydrodipicolinate N-succinyltransferase
- EC
- 2.3.1.117
- UniProt
- P56220
- Ligands
- COA, NPI
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 274 | 24% helix, 30% strand | P56220 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 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 | 0.32 | 0.77 | 10 | empty |
| 2 | 53 | 0.31 | 0.76 | 18 | empty |
Compared structures
- 2TDT · Complex of tetrahydrodipicolinate N-succinyltransferase with 2-aminopimelate and coenzyme… · the same entry in another collection · chain A against A, TM-score 1.00
- P56220 · AlphaFold monomer V2.0 prediction for 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P56220
- Elsewhere: RCSB PDB 2TDT · PDBe 2TDT · UniProt P56220
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