MolNFT v1 · #129219 · protein

Plla lectin, monosaccharide complex

5ODU: “Plla lectin, monosaccharide complex”. X-ray diffraction, 2 ligands (AMG, CA), 6 pockets (best druggability 0.56). MolNFT v1 #129219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ODU
Type: protein
Length: 968 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plla
UniProt: Q7N561
Ligands: AMG, CA
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Plla	protein	121	2% helix, 50% strand	Q7N561

Ligands and binding sites

AMG · methyl alpha-D-galactopyranoside · ligand · 8 copies · chains A, B, C, D, E, F, G, H
CA · Calcium 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	341	0.56	0.76	44	empty
2	168	0.48	0.77	27	empty
3	50	0.39	0.80	12	empty
4	75	0.37	0.78	18	empty
5	102	0.35	0.74	17	empty

Interfaces

10 interfaces between chains.

D–H · 1056 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 1048 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1034 Å² buried · 16 hydrogen bonds · protein-protein
B–H · 756 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 299 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5ODU · PllA lectin, monosaccharide complex · the same entry in another collection · chain H against H, TM-score 1.00
Q7N561 · AlphaFold monomer V2.0 prediction for lectin a (Q7N561) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q7N561
Elsewhere: RCSB PDB 5ODU · PDBe 5ODU · UniProt Q7N561

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