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Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 Fab' fragment in complex with GP41 peptide analog ELD(PAF)WAS

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

PDB: 3IDN
Type: protein
Length: 436 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2F5 Fab light chain; 2F5 Fab heavy chain; GP41 mper peptide analog
Pockets: 2 · best druggability 0.58

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2F5 Fab light chain	protein	214	6% helix, 51% strand	—
B	2F5 Fab heavy chain	protein	215	8% helix, 52% strand	—
C	GP41 mper peptide analog	protein	7	0% helix, 14% 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	401	0.58	0.75	50	empty
2	54	0.25	0.73	17	empty

Interfaces

3 interfaces between chains.

A–B · 1798 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 379 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 241 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

3IDN · Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment… · 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 3IDN · PDBe 3IDN

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