MolNFT v1 · #122035 · protein

Crystal structure of CGL1 from crassostrea gigas, mannose-bound form (CGL1/MAN2)

5IDB · Natterin-3: “Crystal structure of CGL1 from crassostrea gigas, mannose-bound form (CGL1/MAN2)”. X-ray diffraction, 2 ligands (BMA, MAN), 1 pocket (best druggability 0.78). MolNFT v1 #122035 on GenesisL1: 3D structure, binding sites…

PDB: 5IDB
Type: protein
Length: 284 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Natterin-3
UniProt: K1QRB6
Ligands: BMA, MAN
Pockets: 1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Natterin-3	protein	142	0% helix, 63% strand	K1QRB6

Ligands and binding sites

BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, A
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B, A
NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.78	0.89	41	empty

Interfaces

1 interface between chains.

B–A · 1199 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5IDB · Crystal structure of CGL1 from Crassostrea gigas, mannose-bound form (CGL1/MAN2) · the same entry in another collection · chain B against B, 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 K1QRB6
Elsewhere: RCSB PDB 5IDB · PDBe 5IDB · UniProt K1QRB6

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