MolNFT v1 · #31840 · protein

Fava bean lectin-glucose complex

2B7Y · Favin beta chain: “Fava bean lectin-glucose complex”. X-ray diffraction, 4 ligands (GLC, NAG, MN), 1 pocket (best druggability 0.52). MolNFT v1 #31840 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2B7Y
Type: protein
Length: 456 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Favin beta chain; Favin alpha chain
UniProt: P02871
Ligands: GLC, NAG, MN, CA
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Favin beta chain	protein	181	2% helix, 43% strand	P02871
B, D	Favin alpha chain	protein	47	6% helix, 60% strand	P02871

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
MN · Manganese (II) ion · metal · 2 copies · chains A, C
CA · Calcium ion · metal · 2 copies · chains A, C

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	88	0.52	0.84	17	empty

Interfaces

5 interfaces between chains.

A–B · 3889 Å² buried · 90 hydrogen bonds · protein-protein
C–D · 3876 Å² buried · 109 hydrogen bonds · protein-protein
A–C · 869 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 162 Å² buried · 1 hydrogen bond · protein-protein
B–C · 131 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 glycan (N-glycosylation).

Compared structures

2B7Y · Fava Bean Lectin-Glucose Complex · the same entry in another collection · chain A against A, TM-score 1.00
P02871 · AlphaFold monomer V2.0 prediction for favin (P02871) · a predicted model of the same protein · chain A 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 P02871
Elsewhere: RCSB PDB 2B7Y · PDBe 2B7Y · UniProt P02871

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