Research workbench

Crystal structure analysis of maclura pomifera agglutinin complex with P-nitrophenyl-galnac

Analyse Crystal structure analysis of maclura pomifera agglutinin complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LM1
Type: protein
Length: 1,181 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agglutinin alpha chain; Agglutinin beta-2 chain
UniProt: P18674, P18676
Ligands: LEC
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M, O	Agglutinin alpha chain	protein	133	0% helix, 67% strand	P18674
B, F, H, N, P	Agglutinin beta-2 chain	protein	15	0% helix, 40% strand	P18676
D, J, L	Agglutinin beta-2 chain	protein	14	0% helix, 43% strand	P18676

Ligands and binding sites

LEC · 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside · ligand · 7 copies · chains A, C, G, E, I, K, M

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

Pockets

20 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	434	0.86	0.93	49	empty
2	426	0.85	0.93	49	empty
3	742	0.71	0.77	73	LEC
4	637	0.68	0.77	64	LEC
5	262	0.60	0.79	28	empty

Interfaces

49 interfaces between chains.

C–D · 548 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 537 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 533 Å² buried · 7 hydrogen bonds · protein-protein
K–L · 529 Å² buried · 7 hydrogen bonds · protein-protein
I–J · 525 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3LM1 · Crystal Structure Analysis of Maclura pomifera agglutinin complex with… · the same entry in another collection · chain P against P, 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 P18674
Every structure of UniProt P18676
Elsewhere: RCSB PDB 3LM1 · PDBe 3LM1 · UniProt P18674 · UniProt P18676

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