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Crystal structure of cyanovirin-N complexed to a synthetic hexamannoside

Analyse Crystal structure of cyanovirin-N complexed to a synthetic hexamannoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GXY
Type: protein
Length: 202 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyanovirin-N
UniProt: P81180
Ligands: OPM, MAN, MG
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cyanovirin-N	protein	101	13% helix, 55% strand	P81180

Ligands and binding sites

OPM · pentyl alpha-D-mannopyranoside · ligand · 2 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
MG · Magnesium ion · metal · chains A, B
NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	162	0.54	0.80	26	empty

Interfaces

1 interface between chains.

A–B · 3287 Å² buried · 61 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3GXY · Crystal structure of cyanovirin-n complexed to a synthetic hexamannoside · the same entry in another collection · chain A against A, TM-score 1.00
P81180 · AlphaFold monomer V2.0 prediction for cyanovirin-N (P81180) · a predicted model of the same protein · chain B against A, TM-score 0.49

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P81180
Elsewhere: RCSB PDB 3GXY · PDBe 3GXY · UniProt P81180

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