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Linb complexed with clindamycin and ampcpp

Analyse Linb complexed with clindamycin and ampcpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JZ0
Type: protein
Length: 532 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lincosamide nucleotidyltransferase
UniProt: Q9WVY4
Ligands: APC, CLY, MG
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lincosamide nucleotidyltransferase	protein	266	54% helix, 14% strand	Q9WVY4

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
CLY · Clindamycin · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 5 copies · chains A, B

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

Pockets

2 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	514	0.74	0.82	50	MG, APC, CLY
2	526	0.73	0.82	58	MG, APC, CLY

Interfaces

1 interface between chains.

A–B · 2609 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

3JZ0 · LinB complexed with clindamycin and AMPCPP · 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 Q9WVY4
Elsewhere: RCSB PDB 3JZ0 · PDBe 3JZ0 · UniProt Q9WVY4

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