MolNFT v1 · #99431 · protein

Structure of a binary complex between homologous tetrameric legume lectins from butea monosperma and spatholobus parviflorus seeds

4M3C · Lectin alpha chain: “Structure of a binary complex between homologous tetrameric legume lectins from butea monosperma and…”. X-ray diffraction, 3 ligands (ABU, CA, MN), 9 pockets (best druggability 0.81). MolNFT v1 #99431 on…

PDB: 4M3C
Type: protein
Length: 1,952 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin alpha chain; Lectin beta chain; Seed lectin alpha chain; Seed lectin beta chain
UniProt: H2L2M6, H2L2M7, P86352, P86353
Ligands: ABU, CA, MN
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Lectin alpha chain	protein	249	8% helix, 43% strand	H2L2M6
B, D	Lectin beta chain	protein	239	5% helix, 45% strand	H2L2M7
E, G	Seed lectin alpha chain	protein	249	6% helix, 44% strand	P86352
F, H	Seed lectin beta chain	protein	239	4% helix, 45% strand	P86353

Ligands and binding sites

ABU · Gamma-amino-butanoic acid · ligand · 6 copies · chains A, D, B, C, E, 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
GOL · Glycerol · additive · 3 copies · chains C, D, E, F

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	535	0.81	0.87	65	empty
2	415	0.80	0.89	48	GOL
3	537	0.80	0.87	63	GOL
4	560	0.78	0.84	72	empty
5	517	0.77	0.84	47	empty

Interfaces

13 interfaces between chains.

B–C · 1070 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 1043 Å² buried · 20 hydrogen bonds · protein-protein
E–H · 1021 Å² buried · 22 hydrogen bonds · protein-protein
F–G · 1010 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 962 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4M3C · Structure of a binary complex between homologous tetrameric legume lectins from Butea… · the same entry in another collection · chain H against H, TM-score 1.00
P86353 · AlphaFold monomer V2.0 prediction for seed lectin beta chain (P86353) · a predicted model of the same protein · chain F 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 H2L2M6
Every structure of UniProt H2L2M7
Every structure of UniProt P86352
Every structure of UniProt P86353
Elsewhere: RCSB PDB 4M3C · PDBe 4M3C · UniProt H2L2M6 · UniProt H2L2M7 · UniProt P86352 · UniProt P86353

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.