Research workbench

Concanavalin a complex with 4'-nitrophenyl-alpha-D-mannopyranoside

Analyse Concanavalin a complex with 4'-nitrophenyl-alpha-D-mannopyranoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VAM
Type: protein
Length: 948 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin a
UniProt: P02866
Ligands: PNA, MN, CA
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Concanavalin a	protein	237	5% helix, 48% strand	P02866

Ligands and binding sites

PNA · 4-nitrophenyl alpha-D-mannopyranoside · ligand · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

8 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	314	0.81	0.92	53	empty
2	315	0.79	0.90	55	empty
3	319	0.79	0.90	55	empty
4	50	0.70	0.98	18	empty
5	169	0.69	0.88	42	empty

Interfaces

6 interfaces between chains.

A–B · 1143 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1135 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1112 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1059 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 67 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1VAM · Concanavalin a complex with 4'-nitrophenyl-alpha-D-mannopyranoside · the same entry in another collection · chain D against D, TM-score 1.00
P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain A 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 1VAM · PDBe 1VAM · UniProt P02866

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