MolNFT v1 · #177506 · protein

Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide

7EKK · Heavy chain of the Fab region of delta-loop variant of…: “Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide”. X-ray diffraction, 3 ligands (SO4, NH4, CL), 2 pockets (best druggability 0.58).…

PDB: 7EKK
Type: protein
Length: 444 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain of the Fab region of delta-loop variant of anti-HIV-1 broadly neutralizing…
Ligands: SO4, NH4, CL
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Heavy chain of the Fab region of delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide	protein	218	7% helix, 55% strand	—
L	Light chain of the Fab region of delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide	protein	212	7% helix, 49% strand	—
P	Mper region of the envelope glycoprotein GP41 from HIV-1	protein	14	79% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains H
NH4 · Ammonium ion · ion · chains H
CL · Chloride ion · ion · chains L
GOL · Glycerol · additive · 4 copies · chains H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	445	0.58	0.74	46	empty
2	111	0.42	0.77	21	GOL

Interfaces

3 interfaces between chains.

H–L · 1626 Å² buried · 12 hydrogen bonds · protein-protein
H–P · 577 Å² buried · 6 hydrogen bonds · protein-protein
L–P · 217 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7EKK · Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide · the same entry in another collection · chain P against P, 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
Elsewhere: RCSB PDB 7EKK · PDBe 7EKK

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