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Crystal structure of diaminopimelate decarboxylase

Analyse Crystal structure of diaminopimelate decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KNW
Type: protein
Length: 421 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diaminopimelate decarboxylase
EC: 4.1.1.20
UniProt: P00861
Ligands: PLP, LI, SO4
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diaminopimelate decarboxylase (EC 4.1.1.20)	protein	421	31% helix, 23% strand	P00861

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · chains A
LI · Lithium ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	456	0.61	0.76	47	SO4, PLP, MES
2	69	0.33	0.76	17	empty
3	55	0.28	0.75	16	empty

Modifications

Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).

Compared structures

1KNW · Crystal structure of diaminopimelate decarboxylase · the same entry in another collection · chain A against A, TM-score 1.00
P00861 · AlphaFold monomer V2.0 prediction for diaminopimelate decarboxylase (P00861) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P00861
Elsewhere: RCSB PDB 1KNW · PDBe 1KNW · UniProt P00861

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