MolNFT v1 · #67209 · protein

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

3IDM · 2F5 Fab light chain: “Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 Fab' fragment in complex with GP41…”. X-ray diffraction, 3 pockets (best druggability 0.58). MolNFT v1 #67209 on GenesisL1: 3D…

PDB: 3IDM
Type: protein
Length: 448 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: 3 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 6% 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	227	7% helix, 52% strand	—
C	GP41 mper 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	408	0.58	0.75	51	empty
2	204	0.47	0.74	31	empty
3	71	0.31	0.74	17	empty

Interfaces

3 interfaces between chains.

A–B · 1877 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 400 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 249 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3IDM · 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 3IDM · PDBe 3IDM

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