Research workbench

HIV-1 antibody 2F5 in complex with epitope scaffold ES2

Analyse HIV-1 antibody 2F5 in complex with epitope scaffold ES2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LEV
Type: protein
Length: 628 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA polymerase sigma factor; 2F5 antibody light chain; 2F5 antibody heavy chain
UniProt: Q9EZJ8
Ligands: ATP
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA polymerase sigma factor	protein	177	66% helix, 1% strand	Q9EZJ8
L	2F5 antibody light chain	protein	214	5% helix, 48% strand	—
H	2F5 antibody heavy chain	protein	237	6% helix, 48% strand	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A, H
1PE · Pentaethylene glycol · additive · chains L, H
GOL · Glycerol · additive · chains A, L, H

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

Pockets

7 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	621	0.63	0.74	64	1PE
2	105	0.55	0.84	23	empty
3	148	0.51	0.79	24	empty
4	179	0.50	0.77	32	empty
5	157	0.43	0.75	26	empty

Interfaces

3 interfaces between chains.

L–H · 2041 Å² buried · 18 hydrogen bonds · protein-protein
A–H · 542 Å² buried · 6 hydrogen bonds · protein-protein
A–L · 354 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3LEV · HIV-1 antibody 2F5 in complex with epitope scaffold ES2 · the same entry in another collection · chain A against A, TM-score 1.00
Q9EZJ8 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (Q9EZJ8) · a predicted model of the same protein · chain A against A, TM-score 0.86

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 Q9EZJ8
Elsewhere: RCSB PDB 3LEV · PDBe 3LEV · UniProt Q9EZJ8

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