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Crystal structure of rabbit mab R20 Fab in complex with V3 C-terminus of HIV-1 consensus B GP120

Analyse Crystal structure of rabbit mab R20 Fab in complex with V3 C-terminus of HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JO3
Type: protein
Length: 900 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monoclonal anti-HIV-1 GP120 V3 antibody R20 light chain; Monoclonal anti-HIV-1 GP120 V3…
UniProt: Q9YY05
Ligands: SO4
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Monoclonal anti-HIV-1 GP120 V3 antibody R20 light chain	protein	214	8% helix, 53% strand	—
H, I	Monoclonal anti-HIV-1 GP120 V3 antibody R20 heavy chain	protein	227	4% helix, 56% strand	—
P, Q	GP120	protein	9	33% helix, 22% strand	Q9YY05

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains M

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

Pockets

8 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	649	0.77	0.83	66	empty
2	778	0.66	0.74	70	empty
3	252	0.58	0.79	32	empty
4	122	0.41	0.75	21	empty
5	69	0.34	0.76	17	empty

Interfaces

10 interfaces between chains.

M–I · 1989 Å² buried · 19 hydrogen bonds · protein-protein
L–H · 1988 Å² buried · 16 hydrogen bonds · protein-protein
H–P · 603 Å² buried · 9 hydrogen bonds · protein-protein
I–Q · 588 Å² buried · 9 hydrogen bonds · protein-protein
L–I · 466 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

4JO3 · Crystal structure of rabbit mAb R20 Fab in complex with V3 C-terminus of HIV-1 Consensus… · 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
Every structure of UniProt Q9YY05
Elsewhere: RCSB PDB 4JO3 · PDBe 4JO3 · UniProt Q9YY05

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