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Crystal structure of a putative gamma-D-glutamyl-L-diamino acid endopeptidase (NPUN_R0659) from nostoc punctiforme pcc 73102 at 1.60 a resolution

Analyse Crystal structure of a putative gamma-D-glutamyl-L-diamino acid endopeptidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EVR
Type: protein
Length: 222 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: COG0791: cell wall-associated hydrolases (invasion- associated proteins)
UniProt: B2J9B4
Ligands: NA, CL
Pockets: 2 · best druggability 0.40

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	COG0791: cell wall-associated hydrolases (invasion- associated proteins)	protein	222	24% helix, 32% strand	B2J9B4

Ligands and binding sites

NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 5 copies · 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	114	0.40	0.76	26	empty
2	62	0.30	0.75	12	empty

Modifications

Observed in the structure: 2 modified (engineered).

Compared structures

2EVR · Crystal structure of a putative gamma-D-glutamyl-L-diamino acid endopeptidase… · the same entry in another collection · 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 B2J9B4
Elsewhere: RCSB PDB 2EVR · PDBe 2EVR · UniProt B2J9B4

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