MolNFT v1 · #48055 · protein

Pterocarpus angolensis lectin complexed with man-6

2PHF: “Pterocarpus angolensis lectin complexed with man-6”. X-ray diffraction, 4 ligands (MAN, BMA, MN), 2 pockets (best druggability 0.33). MolNFT v1 #48055 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PHF
Type: protein
Length: 480 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: Q8GSD2
Ligands: MAN, BMA, MN, CA
Pockets: 2 · best druggability 0.33

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lectin	protein	240	5% helix, 47% strand	Q8GSD2

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · chains B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
CA · Calcium ion · metal · 2 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	58	0.33	0.77	16	empty
2	52	0.32	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 921 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cyclization).

Compared structures

2PHF · Pterocarpus angolensis lectin complexed with Man-6 · 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 Q8GSD2
Elsewhere: RCSB PDB 2PHF · PDBe 2PHF · UniProt Q8GSD2

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