MolNFT v1 · #25303 · protein

A triclinic crystal form of the lectin concanavalin a

1VLN: “A triclinic crystal form of the lectin concanavalin a”. X-ray diffraction, 2 ligands (MN, CA), 15 pockets (best druggability 0.87). MolNFT v1 #25303 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VLN
Type: protein
Length: 1,896 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin a
UniProt: P08902
Ligands: MN, CA
Pockets: 15 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Concanavalin a	protein	237	4% helix, 44% strand	P08902

Ligands and binding sites

MN · Manganese (II) ion · metal · 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

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1077	0.87	0.88	146	empty
2	806	0.85	0.88	114	empty
3	187	0.77	0.93	35	empty
4	75	0.72	0.97	23	empty
5	55	0.72	0.99	18	empty

Interfaces

11 interfaces between chains.

E–G · 1157 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1155 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1154 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1149 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1142 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

1VLN · A triclinic crystal form of the lectin concanavalin a · the same entry in another collection · chain H against H, TM-score 1.00
P08902 · AlphaFold monomer V2.0 prediction for lectin alpha chain (P08902) · a predicted model of the same protein · chain A 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 1VLN · PDBe 1VLN · UniProt P08902

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