MolNFT v1 · #37816 · protein

Crystal structure of dioclea violacea seed lectin

2GDF: “Crystal structure of dioclea violacea seed lectin”. X-ray diffraction, 2 ligands (MN, CA), 4 pockets (best druggability 0.84). MolNFT v1 #37816 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GDF
Type: protein
Length: 926 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: P08902
Ligands: MN, CA
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Lectin	protein	226	3% helix, 47% strand	P08902
B, D	Lectin	protein	237	4% helix, 47% strand	P08902

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains B, D
CA · Calcium ion · metal · 2 copies · chains B, D

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

Pockets

4 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	1089	0.84	0.86	136	empty
2	92	0.47	0.81	24	empty
3	52	0.46	0.86	17	empty
4	79	0.45	0.81	22	empty

Interfaces

4 interfaces between chains.

A–B · 1017 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1015 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 840 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 831 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2GDF · Crystal structure of Dioclea violacea seed lectin · the same entry in another collection · chain A against A, TM-score 1.00
P08902 · AlphaFold monomer V2.0 prediction for lectin alpha chain (P08902) · 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 P08902
Elsewhere: RCSB PDB 2GDF · PDBe 2GDF · UniProt P08902

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