MolNFT v1 · #103499 · protein

Crystal structure of banana lectin bound to dimannose

4PIK · Ripening-associated protein: “Crystal structure of banana lectin bound to dimannose”. X-ray diffraction, 1 ligand (MAN), 3 pockets (best druggability 0.75). MolNFT v1 #103499 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4PIK
Type: protein
Length: 565 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ripening-associated protein
UniProt: O22321
Ligands: MAN
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 70% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ripening-associated protein	protein	140	0% helix, 72% strand	O22321
B, D	Ripening-associated protein	protein	142	0% helix, 68% strand	O22321
C	Ripening-associated protein	protein	141	0% helix, 71% strand	O22321

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 11 copies · chains B, C, D, A
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	648	0.75	0.81	58	GOL
2	90	0.43	0.79	16	GOL
3	122	0.43	0.76	23	GOL

Interfaces

5 interfaces between chains.

C–D · 798 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 780 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 440 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 414 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 325 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4PIK · Crystal Structure of Banana Lectin bound to dimannose · 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 O22321
Elsewhere: RCSB PDB 4PIK · PDBe 4PIK · UniProt O22321

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