MolNFT v1 · #82635 · protein

Crystal structure of CT1,3GAL43A in complex with isopropy-beta-D- thiogalactoside

3VT2 · Ricin B lectin: “Crystal structure of CT1,3GAL43A in complex with isopropy-beta-D- thiogalactoside”. X-ray diffraction, 1 ligand (IPT), 20 pockets (best druggability 0.80). MolNFT v1 #82635 on GenesisL1: 3D structure, binding sites…

PDB: 3VT2
Type: protein
Length: 2,787 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ricin B lectin
UniProt: A3DD67
Ligands: IPT
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F	Ricin B lectin	protein	461	6% helix, 49% strand	A3DD67
C	Ricin B lectin	protein	482	6% helix, 46% strand	A3DD67

Ligands and binding sites

IPT · 1-methylethyl 1-thio-beta-D-galactopyranoside · ligand · 7 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 7 copies · chains A, B, C, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	193	0.80	0.94	33	GOL
2	542	0.73	0.82	56	empty
3	774	0.70	0.77	72	empty
4	762	0.69	0.76	70	empty
5	68	0.67	0.94	19	empty

Interfaces

7 interfaces between chains.

C–F · 1152 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 742 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 682 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 672 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 672 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3VT2 · Crystal structure of Ct1,3Gal43A in complex with isopropy-beta-D-thiogalactoside · 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 A3DD67
Elsewhere: RCSB PDB 3VT2 · PDBe 3VT2 · UniProt A3DD67

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