MolNFT v1 · #8749 · protein

Native dioclea guianensis seed lectin

1H9W: “Native dioclea guianensis seed lectin”. X-ray diffraction, 2 ligands (MN, CA), 2 pockets (best druggability 0.64). MolNFT v1 #8749 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1H9W
Type: protein
Length: 462 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Seed lectin
UniProt: P81637
Ligands: MN, CA
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Seed lectin	protein	232	4% helix, 46% strand	P81637
B	Seed lectin	protein	230	4% helix, 45% strand	P81637

Ligands and binding sites

MN · Manganese (II) ion · metal · 7 copies · chains A, B
CA · Calcium ion · metal · 3 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	75	0.64	0.91	24	MN
2	74	0.57	0.88	27	MN

Interfaces

1 interface between chains.

A–B · 1048 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

1H9W · Native Dioclea Guianensis seed lectin · the same entry in another collection · chain A against A, TM-score 1.00
P81637 · AlphaFold monomer V2.0 prediction for lectin alpha chain (P81637) · 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 P81637
Elsewhere: RCSB PDB 1H9W · PDBe 1H9W · UniProt P81637

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