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Crystal structure of GP1 - the receptor binding domain of lassa virus

Analyse Crystal structure of GP1 - the receptor binding domain of lassa virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZJF
Type: protein
Length: 636 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoprotein
UniProt: A0A097F5U5
Ligands: NAG
Pockets: 9 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Glycoprotein	protein	161	22% helix, 29% strand	A0A097F5U5
B, D	Glycoprotein	protein	157	22% helix, 28% strand	A0A097F5U5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, D, C

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	290	0.61	0.80	39	empty
2	273	0.61	0.80	36	empty
3	103	0.38	0.75	24	empty
4	92	0.35	0.74	20	empty
5	103	0.33	0.73	17	empty

Interfaces

4 interfaces between chains.

A–B · 509 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 496 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 308 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 289 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 glycan, 12 disulfide (N-glycosylation, disulfide).

Compared structures

4ZJF · Crystal structure of GP1 - the receptor binding domain of Lassa virus · 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 A0A097F5U5
Elsewhere: RCSB PDB 4ZJF · PDBe 4ZJF · UniProt A0A097F5U5

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