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Crystal structure of dmsp lyase rddddp from roseobacter denitrificans

Analyse Crystal structure of dmsp lyase rddddp from roseobacter denitrificans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4B28
Type: protein
Length: 437 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallopeptidase, family M24, putative
UniProt: Q166H0
Ligands: FE
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallopeptidase, family M24, putative	protein	437	39% helix, 19% strand	Q166H0

Ligands and binding sites

FE · Fe (III) ion · metal · 2 copies · 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	117	0.59	0.85	26	empty

Compared structures

4B28 · Crystal structure of DMSP lyase RdDddP from Roseobacter denitrificans · the same entry in another collection · chain A against A, TM-score 1.00
Q166H0 · AlphaFold monomer V2.0 prediction for dimethylsulfonioproprionate lyase dddp (Q166H0) · a predicted model of the same protein · 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 Q166H0
Elsewhere: RCSB PDB 4B28 · PDBe 4B28 · UniProt Q166H0

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