MolNFT v1 · #138240 · protein

Structure of a bacterial polysialyltransferase in complex with cdp

5WCN · Siad: “Structure of a bacterial polysialyltransferase in complex with cdp”. X-ray diffraction, 2 ligands (CDP, SO4), 7 pockets (best druggability 0.70). MolNFT v1 #138240 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WCN
Type: protein
Length: 764 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Siad
UniProt: G4RIN4
Ligands: CDP, SO4
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
M, A	Siad	protein	382	46% helix, 16% strand	G4RIN4

Ligands and binding sites

CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains M, A
SO4 · Sulfate ion · ion · 2 copies · chains M, A

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	807	0.70	0.76	63	CDP
2	263	0.65	0.82	30	empty
3	348	0.55	0.75	50	CDP
4	77	0.38	0.78	16	empty
5	75	0.34	0.75	11	empty

Interfaces

1 interface between chains.

M–A · 1185 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5WCN · Structure of a bacterial polysialyltransferase in complex with CDP · the same entry in another collection · chain M against M, 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 G4RIN4
Elsewhere: RCSB PDB 5WCN · PDBe 5WCN · UniProt G4RIN4

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