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The dolichos biflorus seed lectin in complex with adenine

Analyse The dolichos biflorus seed lectin in complex with adenine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BJQ
Type: protein
Length: 1,940 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: P05045
Ligands: ADE, CA, MN
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Lectin	protein	251	8% helix, 45% strand	P05045
B, H	Lectin	protein	253	8% helix, 45% strand	P05045
C, D, E, F	Lectin	protein	233	6% helix, 49% strand	P05045

Ligands and binding sites

ADE · Adenine · ligand · 8 copies · chains A, C, B, D, E, G, F, H
CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1171	0.86	0.87	116	ADE
2	341	0.83	0.92	55	ADE
3	331	0.82	0.93	54	ADE
4	1138	0.82	0.84	120	empty
5	427	0.81	0.89	59	ADE

Interfaces

11 interfaces between chains.

A–C · 1137 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 1136 Å² buried · 11 hydrogen bonds · protein-protein
F–H · 1129 Å² buried · 13 hydrogen bonds · protein-protein
E–G · 1128 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 903 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

1BJQ · The dolichos biflorus seed lectin in complex with adenine · the same entry in another collection · chain H against H, TM-score 1.00
P05045 · AlphaFold monomer V2.0 prediction for seed lectin subunit I (P05045) · a predicted model of the same protein · chain C 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 P05045
Elsewhere: RCSB PDB 1BJQ · PDBe 1BJQ · UniProt P05045

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