MolNFT v1 · #134808 · protein

Crystal structure of the dimethylsulfoniopropionate (dmsp) lyase dddk complexed with nickel and diacrylate

5TFZ · Dimethylsulfoniopropionate lyase dddk: “Crystal structure of the dimethylsulfoniopropionate (dmsp) lyase dddk complexed with nickel and diacrylate”. X-ray diffraction, 2 ligands (7BC, NI), 3 pockets (best druggability 0.65). MolNFT…

PDB: 5TFZ
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dimethylsulfoniopropionate lyase dddk
UniProt: Q4FNM4
Ligands: 7BC, NI
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dimethylsulfoniopropionate lyase dddk	protein	127	9% helix, 48% strand	Q4FNM4
B	Dimethylsulfoniopropionate lyase dddk	protein	131	8% helix, 47% strand	Q4FNM4

Ligands and binding sites

7BC · 3-(acryloyloxy)propanoic acid · ligand · 2 copies · chains A, B
NI · Nickel (II) ion · metal · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	78	0.65	0.90	15	NI, 7BC
2	82	0.64	0.90	18	7BC
3	108	0.41	0.76	23	PEG

Interfaces

1 interface between chains.

A–B · 1604 Å² buried · 19 hydrogen bonds · protein-protein

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 Q4FNM4
Elsewhere: RCSB PDB 5TFZ · PDBe 5TFZ · UniProt Q4FNM4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.