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Structure of human intelectin-1 in complex with allyl-beta- galactofuranose

Analyse Structure of human intelectin-1 in complex with allyl-beta- galactofuranose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WMY
Type: protein
Length: 564 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Intelectin-1
UniProt: Q8WWA0
Ligands: 3S6, CA
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Intelectin-1	protein	283	19% helix, 26% strand	Q8WWA0
B	Intelectin-1	protein	281	17% helix, 26% strand	Q8WWA0

Ligands and binding sites

3S6 · prop-2-en-1-yl beta-D-galactofuranoside · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 6 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.38	0.80	22	empty
2	58	0.36	0.79	18	3S6

Interfaces

1 interface between chains.

A–B · 604 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

4WMY · Structure of Human intelectin-1 in complex with allyl-beta-galactofuranose · the same entry in another collection · chain A against A, TM-score 1.00
Q8WWA0 · AlphaFold monomer V2.0 prediction for intelectin-1 (Q8WWA0) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q8WWA0
Elsewhere: RCSB PDB 4WMY · PDBe 4WMY · UniProt Q8WWA0

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