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Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in complex with GP41 peptide analog E-[dap]- dkwqs (cyclic)

Analyse Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1U92
Type: protein
Length: 445 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody 2F5 (light chain); Antibody 2F5 (heavy chain); GP41 peptide analog
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody 2F5 (light chain)	protein	214	6% helix, 51% strand	—
B	Antibody 2F5 (heavy chain)	protein	224	8% helix, 51% strand	—
C	GP41 peptide analog	protein	7	0% helix, 14% strand	—

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	371	0.57	0.75	46	empty
2	160	0.43	0.74	27	empty
3	56	0.28	0.74	15	empty

Interfaces

3 interfaces between chains.

A–B · 1824 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 374 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 236 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1U92 · Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1U92 · PDBe 1U92

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