MolNFT v1 · #68052 · protein

Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus

3J4P · Capsid protein VP1: “Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of…”. Electron microscopy, 4 ligands (GU4, YYJ, NA), 7 pockets (best druggability 0.64). MolNFT v1 #68052 on GenesisL1…

PDB: 3J4P
Type: protein
Length: 517 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1
Ligands: GU4, YYJ, NA, MG
Pockets: 7 · best druggability 0.64

Structure

electron microscopy · 1 distinct chain · 3% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	517	3% helix, 28% strand	—

Ligands and binding sites

GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · chains A
YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · chains A
NA · Sodium ion · metal
MG · Magnesium ion · metal

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

Pockets

7 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	586	0.64	0.75	64	empty
2	155	0.46	0.76	18	empty
3	118	0.41	0.76	21	empty
4	113	0.38	0.74	20	empty
5	125	0.36	0.73	20	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

3J4P · Electron Microscopy Analysis of a Disaccharide Analog complex Reveals Receptor… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3J4P · PDBe 3J4P

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