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Fab structure of rabbit monoclonal antibody R53 targeting an epitope in HIV-1 GP120 C4 region

Analyse Fab structure of rabbit monoclonal antibody R53 targeting an epitope in HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZTP
Type: protein
Length: 439 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain of Fab fragment of rabbit monoclonal antibody R53; Heavy chain of Fab…
Pockets: 6 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Light chain of Fab fragment of rabbit monoclonal antibody R53	protein	216	7% helix, 55% strand	—
H	Heavy chain of Fab fragment of rabbit monoclonal antibody R53	protein	223	5% helix, 51% strand	—

Pockets

6 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	432	0.57	0.74	49	empty
2	55	0.57	0.90	17	empty
3	55	0.54	0.89	21	empty
4	163	0.46	0.76	33	empty
5	54	0.27	0.73	15	empty

Interfaces

1 interface between chains.

L–H · 1958 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

4ZTP · Fab structure of rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4… · the same entry in another collection · chain L against L, 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 4ZTP · PDBe 4ZTP

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