MolNFT v1 · #125538 · protein

Structural basis of zika and dengue virus potent antibody cross- neutralization

5LBS · Envelope protein E: “Structural basis of zika and dengue virus potent antibody cross- neutralization”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.65). MolNFT v1 #125538 on GenesisL1: 3D structure, binding…

PDB: 5LBS
Type: protein
Length: 1,246 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope protein E; Broadly neutralizing human antibody EDE1 C8
UniProt: A0A120IIH9
Ligands: SO4
Pockets: 14 · best druggability 0.65

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Envelope protein E	protein	394	8% helix, 50% strand	A0A120IIH9
B	Envelope protein E	protein	386	9% helix, 50% strand	A0A120IIH9
H	Broadly neutralizing human antibody EDE1 C8	protein	121	5% helix, 51% strand	—
I	Broadly neutralizing human antibody EDE1 C8	protein	122	5% helix, 51% strand	—
L	Broadly neutralizing human antibody EDE1 C8	protein	111	3% helix, 47% strand	—
M	Broadly neutralizing human antibody EDE1 C8	protein	112	3% helix, 46% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, I
EDO · 1,2-ethanediol · additive · 11 copies · chains A, H, I, L, M, B

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

Pockets

14 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	647	0.65	0.75	60	EDO
2	493	0.59	0.74	49	empty
3	237	0.46	0.73	35	empty
4	115	0.45	0.77	19	empty
5	63	0.40	0.80	21	empty

Interfaces

7 interfaces between chains.

I–M · 926 Å² buried · 7 hydrogen bonds · protein-protein
H–L · 901 Å² buried · 7 hydrogen bonds · protein-protein
A–L · 248 Å² buried · 6 hydrogen bonds · protein-protein
B–M · 236 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 157 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5LBS · structural basis of Zika and Dengue virus potent antibody cross-neutralization · the same entry in another collection · chain M against M, 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 A0A120IIH9
Elsewhere: RCSB PDB 5LBS · PDBe 5LBS · UniProt A0A120IIH9

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