Research workbench

HIV-1 neutralizing antibody Z13E1 in complex with epitope display protein

Analyse HIV-1 neutralizing antibody Z13E1 in complex with epitope display protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3Q1S
Type: protein
Length: 533 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Z13E1 Fab light chain; Z13E1 Fab heavy chain; Interleukin-22
UniProt: Q9GZX6
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Z13E1 Fab light chain	protein	209	6% helix, 51% strand	—
H	Z13E1 Fab heavy chain	protein	211	6% helix, 54% strand	—
I	Interleukin-22	protein	113	60% helix, 0% strand	Q9GZX6

Ligands and binding sites

GOL · Glycerol · additive · 10 copies · chains L, H, I
IPA · Isopropyl alcohol · additive · 2 copies · chains L

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

Pockets

5 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	435	0.63	0.77	57	GOL
2	281	0.53	0.75	43	empty
3	52	0.50	0.87	21	empty
4	105	0.38	0.75	20	empty
5	51	0.25	0.72	11	empty

Interfaces

3 interfaces between chains.

L–H · 2043 Å² buried · 31 hydrogen bonds · protein-protein
H–I · 731 Å² buried · 11 hydrogen bonds · protein-protein
L–I · 40 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3Q1S · HIV-1 neutralizing antibody Z13e1 in complex with epitope display protein · the same entry in another collection · chain L against L, TM-score 1.00
Q9GZX6 · AlphaFold monomer V2.0 prediction for interleukin-22 (Q9GZX6) · a predicted model of the same protein · chain I against A, TM-score 0.87

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 Q9GZX6
Elsewhere: RCSB PDB 3Q1S · PDBe 3Q1S · UniProt Q9GZX6

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