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Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in complex with GP41 peptide eldkwksl

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: 2PW2
Type: protein
Length: 440 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2F5 Fab' heavy chain; 2F5 Fab' light chain; Peptide epitope
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2F5 Fab' heavy chain	protein	214	5% helix, 51% strand	—
B	2F5 Fab' light chain	protein	221	7% helix, 51% strand	—
C	Peptide epitope	protein	5	0% helix, 20% strand	—

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	384	0.57	0.75	49	empty
2	52	0.27	0.74	14	empty

Interfaces

3 interfaces between chains.

A–B · 1817 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 331 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 229 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2PW2 · 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

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2PW2 · PDBe 2PW2

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