Research workbench

C. glutamicum dap dehydrogenase in complex with dap

Analyse C. glutamicum dap dehydrogenase in complex with dap in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DAP
Type: protein
Length: 320 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diaminopimelic acid dehydrogenase
EC: 1.4.1.16
UniProt: P04964
Ligands: API
Pockets: 1 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diaminopimelic acid dehydrogenase (EC 1.4.1.16)	protein	320	38% helix, 27% strand	P04964

Ligands and binding sites

API · 2,6-diaminopimelic acid · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	500	0.73	0.82	42	API

Compared structures

2DAP · C. glutamicum dap dehydrogenase in complex with dap · the same entry in another collection · chain A against A, TM-score 1.00
P04964 · AlphaFold monomer V2.0 prediction for meso-diaminopimelate D-dehydrogenase (P04964) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P04964
Elsewhere: RCSB PDB 2DAP · PDBe 2DAP · UniProt P04964

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