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Crystal structure of pseudorabies core fragment of glycoprotein H in complex with Fab D6.3

Analyse Crystal structure of pseudorabies core fragment of glycoprotein H in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XQY
Type: protein
Length: 1,796 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein H; A13-D6.3 monoclonal antibody
UniProt: P27416
Ligands: NAG
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Envelope glycoprotein H	protein	464	40% helix, 17% strand	P27416
G, J	A13-D6.3 monoclonal antibody	protein	216	8% helix, 51% strand	—
K, L	A13-D6.3 monoclonal antibody	protein	218	6% helix, 53% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, E, G, J

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	761	0.74	0.79	88	empty
2	761	0.73	0.78	88	empty
3	825	0.69	0.76	62	empty
4	814	0.68	0.75	60	empty
5	485	0.64	0.76	42	empty

Interfaces

7 interfaces between chains.

G–L · 1916 Å² buried · 19 hydrogen bonds · protein-protein
J–K · 1898 Å² buried · 19 hydrogen bonds · protein-protein
E–J · 661 Å² buried · 18 hydrogen bonds · protein-protein
A–G · 650 Å² buried · 17 hydrogen bonds · protein-protein
E–K · 404 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

2XQY · Crystal structure of pseudorabies core fragment of glycoprotein H in complex with Fab D6.3 · 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 P27416
Elsewhere: RCSB PDB 2XQY · PDBe 2XQY · UniProt P27416

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