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Crystal structure of dapd in complex with 2-aminopimelate from corynebacterium glutamicum

Analyse Crystal structure of dapd in complex with 2-aminopimelate from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E3R
Type: protein
Length: 277 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: NPI
Pockets: 2 · best druggability 0.37

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	277	13% helix, 35% strand	Q8NRE3

Ligands and binding sites

NPI · (2S)-2-aminoheptanedioic acid · ligand · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	81	0.37	0.76	17	empty
2	51	0.27	0.75	18	empty

Compared structures

5E3R · Crystal structure of DapD in complex with 2-aminopimelate 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 0.99

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Every structure of UniProt Q8NRE3
Elsewhere: RCSB PDB 5E3R · PDBe 5E3R · UniProt Q8NRE3

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