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Structure of fril, a legume lectin that delays hematopoietic progenitor maturation

Analyse Structure of fril, a legume lectin that delays hematopoietic progenitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QMO
Type: protein
Length: 920 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mannose binding lectin, fril
Ligands: MAN, CA, MN
Pockets: 1 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Mannose binding lectin, fril	protein	113	3% helix, 44% strand	—
E, F, G, H	Mannose binding lectin, fril	protein	117	5% helix, 52% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, E, B, F, C, G, D, H
CA · Calcium ion · metal · 4 copies · chains A, E, B, F, C, G, D, H
MN · Manganese (II) ion · metal · 4 copies · chains E, F, G, H

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	1065	0.76	0.79	112	empty

Interfaces

18 interfaces between chains.

A–E · 4363 Å² buried · 125 hydrogen bonds · protein-protein
D–H · 4352 Å² buried · 125 hydrogen bonds · protein-protein
B–F · 4351 Å² buried · 125 hydrogen bonds · protein-protein
C–G · 4348 Å² buried · 125 hydrogen bonds · protein-protein
C–D · 887 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

1QMO · Structure of FRIL, a legume lectin that delays hematopoietic progenitor maturation · 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
Elsewhere: RCSB PDB 1QMO · PDBe 1QMO

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