Research workbench

Crystal structure of EBV GHGL/CL40/GP42 N-domain

Analyse Crystal structure of EBV GHGL/CL40/GP42 N-domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W0K
Type: protein
Length: 2,410 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein H; Envelope glycoprotein L; CL40 IgG heavy chain; CL40 IgG light…
UniProt: P03231, P03212, P03205
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 9 distinct chains · 20% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Envelope glycoprotein H	protein	655	37% helix, 20% strand	P03231
B	Envelope glycoprotein L	protein	94	35% helix, 15% strand	P03212
H	CL40 IgG heavy chain	protein	213	3% helix, 50% strand	—
L	CL40 IgG light chain	protein	210	7% helix, 49% strand	—
X	Glycoprotein 42	protein	34	0% helix, 3% strand	P03205
D	Envelope glycoprotein L	protein	92	36% helix, 15% strand	P03212
E	CL40 IgG heavy chain	protein	214	3% helix, 50% strand	—
F	CL40 IgG light chain	protein	212	7% helix, 48% strand	—
Y	Glycoprotein 42	protein	31	13% helix, 3% strand	P03205

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	669	0.75	0.81	67	empty
2	205	0.72	0.88	34	empty
3	122	0.72	0.92	25	empty
4	405	0.71	0.82	51	empty
5	753	0.68	0.75	75	empty

Interfaces

16 interfaces between chains.

C–D · 2186 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 2159 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1858 Å² buried · 12 hydrogen bonds · protein-protein
H–L · 1844 Å² buried · 11 hydrogen bonds · protein-protein
A–X · 1802 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide (disulfide).

Compared structures

5W0K · Crystal structure of EBV gHgL/CL40/gp42 N-domain · 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 P03231
Every structure of UniProt P03212
Every structure of UniProt P03205
Elsewhere: RCSB PDB 5W0K · PDBe 5W0K · UniProt P03231 · UniProt P03212 · UniProt P03205

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.