MolNFT v1 · #109410 · protein

Crystal structure of rhdvb P domain in complex with lewis Y

4X1X · VP1: “Crystal structure of rhdvb P domain in complex with lewis Y”. X-ray diffraction, 4 ligands (NDG, GAL, FUC), 1 pocket (best druggability 0.82). MolNFT v1 #109410 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X1X
Type: protein
Length: 666 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
UniProt: I7FLU3
Ligands: NDG, GAL, FUC, CL
Pockets: 1 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	332	7% helix, 39% strand	I7FLU3
B	VP1	protein	334	7% helix, 38% strand	I7FLU3

Ligands and binding sites

NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A, B
GAL · beta-D-galactopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains A, B
CL · Chloride ion · ion · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · 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	1054	0.82	0.84	111	EDO, CL

Interfaces

1 interface between chains.

A–B · 1512 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4X1X · Crystal structure of RHDVb P domain in complex with Lewis Y · 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
Every structure of UniProt I7FLU3
Elsewhere: RCSB PDB 4X1X · PDBe 4X1X · UniProt I7FLU3

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