MolNFT v1 · #30158 · protein

A structure-based mechanism of SARS virus membrane fusion

1ZV8 · E2 glycoprotein: “A structure-based mechanism of SARS virus membrane fusion”. X-ray diffraction, 2 ligands (NA, ZN), 5 pockets (best druggability 0.73). MolNFT v1 #30158 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZV8
Type: protein
Length: 477 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E2 glycoprotein
UniProt: P59594
Ligands: NA, ZN
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	E2 glycoprotein	protein	49	96% helix, 0% strand	P59594
B	E2 glycoprotein	protein	27	63% helix, 0% strand	P59594
C	E2 glycoprotein	protein	46	96% helix, 0% strand	P59594
D	E2 glycoprotein	protein	29	59% helix, 0% strand	P59594
F, J	E2 glycoprotein	protein	30	57% helix, 0% strand	P59594
G, K	E2 glycoprotein	protein	50	96% helix, 0% strand	P59594
H	E2 glycoprotein	protein	34	50% helix, 0% strand	P59594
L	E2 glycoprotein	protein	34	59% helix, 0% strand	P59594

Ligands and binding sites

NA · Sodium ion · metal · 6 copies · chains A, B, G, L, H, F, J, K
ZN · Zinc ion · metal · 2 copies · chains G, H
CAC · Cacodylate ion · additive · chains G, H
ACT · Acetate ion · additive · chains G, H

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.73	0.99	16	empty
2	54	0.73	0.99	17	empty
3	365	0.56	0.75	40	empty
4	82	0.38	0.77	14	empty
5	71	0.31	0.74	13	empty

Interfaces

22 interfaces between chains.

G–L · 1040 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1032 Å² buried · 19 hydrogen bonds · protein-protein
H–I · 1022 Å² buried · 15 hydrogen bonds · protein-protein
J–K · 981 Å² buried · 15 hydrogen bonds · protein-protein
K–L · 978 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1ZV8 · A structure-based mechanism of SARS virus membrane fusion · the same entry in another collection · chain K against K, 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 P59594
Elsewhere: RCSB PDB 1ZV8 · PDBe 1ZV8 · UniProt P59594

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