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Crystal structure of the probable dipeptidase pvdm from pseudomonas aeruginosa

Analyse Crystal structure of the probable dipeptidase pvdm from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B40
Type: protein
Length: 400 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable dipeptidase
UniProt: Q9I187
Ligands: CD, CA, MG
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable dipeptidase	protein	400	47% helix, 14% strand	Q9I187

Ligands and binding sites

CD · Cadmium ion · metal · 2 copies · chains A
CA · Calcium ion · metal · 2 copies · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	427	0.66	0.79	42	empty
2	108	0.52	0.82	24	empty
3	92	0.37	0.76	18	empty
4	86	0.35	0.75	18	empty

Compared structures

3B40 · Crystal structure of the probable dipeptidase PvdM from Pseudomonas aeruginosa · 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 Q9I187
Elsewhere: RCSB PDB 3B40 · PDBe 3B40 · UniProt Q9I187

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