MolNFT v1 · #117294 · protein
Crystal structure of dapd in complex with succinyl-CoA from corynebacterium glutamicum
5E3Q · 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N…: “Crystal structure of dapd in complex with succinyl-CoA from corynebacterium glutamicum”. X-ray diffraction, 1 ligand (SCA), 1 pocket (best druggability 0.35). MolNFT v1 #117294 on…
- PDB
- 5E3Q
- Type
- protein
- Length
- 278 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase
- EC
- 2.3.1.117
- UniProt
- Q8NRE3
- Ligands
- SCA
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 278 | 13% helix, 35% strand | Q8NRE3 |
Ligands and binding sites
- SCA · Succinyl-coenzyme A · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.35 | 0.77 | 18 | empty |
Compared structures
- 5E3Q · Crystal structure of DapD in complex with succinyl-CoA from Corynebacterium glutamicum · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NRE3 · 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 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 Q8NRE3
- Elsewhere: RCSB PDB 5E3Q · PDBe 5E3Q · UniProt Q8NRE3
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