MolNFT v1 · #82612 · protein

Crystal structure of 1,3GAL43A, an exo-beta-1,3-galactanase from clostridium thermocellum

3VSF · Ricin B lectin: “Crystal structure of 1,3GAL43A, an exo-beta-1,3-galactanase from clostridium thermocellum”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #82612 on GenesisL1: 3D structure, binding sites and…

PDB: 3VSF
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
Pockets: 20 · best druggability 0.78

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

GOL · Glycerol · additive · 14 copies · chains A, B, C, D, 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	964	0.78	0.80	98	GOL
2	769	0.77	0.81	91	GOL
3	301	0.67	0.82	38	empty
4	295	0.64	0.81	48	empty
5	576	0.62	0.74	55	empty

Interfaces

7 interfaces between chains.

C–F · 1116 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 705 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 656 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 639 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 633 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3VSF · Crystal structure of 1,3Gal43A, an exo-beta-1,3-Galactanase from Clostridium thermocellum · 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 3VSF · PDBe 3VSF · UniProt A3DD67

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