Research workbench

Anti-HIV-1 Fab 2G12 re-refinement

Analyse Anti-HIV-1 Fab 2G12 re-refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6N32
Type: protein
Length: 862 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 2G12 light chain; Fab 2G12 heavy chain
UniProt: P0DOX7, P0DOX5
Ligands: SO4
Pockets: 11 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab 2G12 light chain	protein	212	7% helix, 53% strand	P0DOX7
H	Fab 2G12 heavy chain	protein	218	9% helix, 52% strand	P0DOX5
M	Fab 2G12 light chain	protein	213	7% helix, 52% strand	P0DOX7
K	Fab 2G12 heavy chain	protein	219	10% helix, 53% strand	P0DOX5

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains L, K, M

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1099	0.76	0.79	121	empty
2	477	0.60	0.75	53	empty
3	163	0.47	0.76	28	SO4
4	139	0.43	0.75	25	empty
5	72	0.34	0.76	15	empty

Interfaces

6 interfaces between chains.

H–K · 973 Å² buried · 14 hydrogen bonds · protein-protein
H–M · 959 Å² buried · 5 hydrogen bonds · protein-protein
L–K · 926 Å² buried · 8 hydrogen bonds · protein-protein
M–K · 925 Å² buried · 9 hydrogen bonds · protein-protein
L–H · 889 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6N32 · Anti-HIV-1 Fab 2G12 re-refinement · the same entry in another collection · chain H against H, TM-score 1.00
P0DOX7 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa light chain (P0DOX7) · a predicted model of the same protein · chain M against A, TM-score 0.82

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 P0DOX7
Every structure of UniProt P0DOX5
Elsewhere: RCSB PDB 6N32 · PDBe 6N32 · UniProt P0DOX7 · UniProt P0DOX5

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