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Crystal structure of leuconostoc citreum nrrl B-1299 N-terminally truncated dextransucrase dsr-M

Analyse Crystal structure of leuconostoc citreum nrrl B-1299 N-terminally truncated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LFC
Type: protein
Length: 2,296 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dsrv
EC: 2.4.1.5
Ligands: CA
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dsrv (EC 2.4.1.5)	protein	1148	24% helix, 21% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	625	0.73	0.80	59	empty
2	114	0.73	0.93	25	empty
3	108	0.71	0.93	24	empty
4	783	0.71	0.77	65	empty
5	475	0.70	0.80	48	GOL

Interfaces

1 interface between chains.

A–B · 445 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5LFC · Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5LFC · PDBe 5LFC

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