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Structure of concanavalin a complexed to beta-D-glcnac (1,2)ALPHA-D- man-(1,6)[BETA-D-GLCNAC(1,2)ALPHA-D-man (1,6)]ALPHA-D-man

Analyse Structure of concanavalin a complexed to beta-D-glcnac (1,2)ALPHA-D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TEI
Type: protein
Length: 1,896 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin a
UniProt: P02866
Ligands: MAN, NAG, MN, CA
Pockets: 10 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Concanavalin a	protein	237	5% helix, 46% strand	P02866

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 24 copies · chains A, B, C, D, E, F, G, H
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 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
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

10 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	1021	0.89	0.90	129	empty
2	998	0.89	0.90	126	empty
3	863	0.74	0.78	83	MAN, NAG
4	50	0.70	0.98	16	empty
5	50	0.70	0.98	17	empty

Interfaces

14 interfaces between chains.

A–B · 1193 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1177 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1168 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1157 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1107 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1TEI · Structure of concanavalin a complexed to beta-D-glcnac… · the same entry in another collection · chain H against H, TM-score 1.00
P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain E against A, TM-score 0.50

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 P02866
Elsewhere: RCSB PDB 1TEI · PDBe 1TEI · UniProt P02866

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