MolNFT v1 · #12439 · protein
Crystal structure of tetrahydrodipicolinate N-succinyltransferase in complex with pimelate and succinyl-CoA
1KGT · 2,3,4,5-tetrahydropyridine-2-carboxylate N…: “Crystal structure of tetrahydrodipicolinate N-succinyltransferase in complex with pimelate and succinyl-CoA”. X-ray diffraction, 2 ligands (PML, SCA), 2 pockets (best druggability 0.34).…
- PDB
- 1KGT
- Type
- protein
- Length
- 274 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase
- EC
- 2.3.1.117
- UniProt
- P56220
- Ligands
- PML, SCA
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 274 | 22% helix, 28% 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 | 52 | 0.34 | 0.79 | 11 | empty |
| 2 | 58 | 0.33 | 0.77 | 14 | empty |
Compared structures
- 1KGT · Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with… · 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 1KGT · PDBe 1KGT · UniProt P56220
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