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Crystal structure of adcc-potent anti-HIV-1 rhesus macaque antibody JR4 Fab

Analyse Crystal structure of adcc-potent anti-HIV-1 rhesus macaque antibody JR4 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RFE
Type: protein
Length: 1,703 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain of adcc-potent anti-HIV-1 antibody JR4; Fab light chain of adcc-potent…
Ligands: CL, SO4
Pockets: 18 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A, E	Fab heavy chain of adcc-potent anti-HIV-1 antibody JR4	protein	215	10% helix, 53% strand	—
L, B	Fab light chain of adcc-potent anti-HIV-1 antibody JR4	protein	210	6% helix, 52% strand	—
C	Fab heavy chain of adcc-potent anti-HIV-1 antibody JR4	protein	214	7% helix, 52% strand	—
D, F	Fab light chain of adcc-potent anti-HIV-1 antibody JR4	protein	212	6% helix, 51% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 9 copies · chains L, B, D, F
SO4 · Sulfate ion · ion · 2 copies · chains H, L, E
GOL · Glycerol · additive · chains E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1121	0.79	0.81	144	CL
2	614	0.63	0.74	56	empty
3	526	0.62	0.75	58	empty
4	201	0.56	0.80	34	empty
5	214	0.55	0.79	39	empty

Interfaces

13 interfaces between chains.

C–D · 1813 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1799 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1727 Å² buried · 13 hydrogen bonds · protein-protein
H–L · 1725 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 680 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4RFE · Crystal structure of ADCC-potent ANTI-HIV-1 Rhesus macaque antibody JR4 Fab · the same entry in another collection · chain H against H, 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 4RFE · PDBe 4RFE

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