MolNFT v1 · #177497 · protein

Crystal structure of 4E10 modified with pyrene acetamide

7EKB · Fab region of the heavy chain of broadly neutralizing…: “Crystal structure of 4E10 modified with pyrene acetamide”. X-ray diffraction, 3 pockets (best druggability 0.58). MolNFT v1 #177497 on GenesisL1: 3D structure, binding sites…

PDB: 7EKB
Type: protein
Length: 443 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab region of the heavy chain of broadly neutralizing antibody anti-HIV-1 4E10; Fab…
Pockets: 3 · best druggability 0.58

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab region of the heavy chain of broadly neutralizing antibody anti-HIV-1 4E10	protein	216	7% helix, 55% strand	—
L	Fab region of the light chain of the broadly neutralizing anti-HIV-1 antibody 4E10	protein	212	7% helix, 49% strand	—
P	Mper region of the HIV-1 envelope glycoprotein protein GP41	protein	15	87% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains H, L
ACT · Acetate ion · additive · chains H

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

Pockets

3 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	460	0.58	0.74	49	GOL
2	138	0.45	0.77	24	empty
3	56	0.31	0.76	16	empty

Interfaces

3 interfaces between chains.

H–L · 1602 Å² buried · 13 hydrogen bonds · protein-protein
H–P · 570 Å² buried · 4 hydrogen bonds · protein-protein
L–P · 216 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7EKB · Crystal structure of 4E10 modified with pyrene acetamide · the same entry in another collection · chain H against H, 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 7EKB · PDBe 7EKB

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