Research workbench

Anti-HIV-1 Fab 2G12 + MAN1-2 re-refinement

Analyse Anti-HIV-1 Fab 2G12 + MAN1-2 re-refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6N35
Type: protein
Length: 860 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: BEZ, MAN
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab 2G12 light chain	protein	211	6% helix, 54% strand	P0DOX7
H, M	Fab 2G12 heavy chain	protein	218	7% helix, 53% strand	P0DOX5
K	Fab 2G12 light chain	protein	213	6% helix, 52% strand	P0DOX7

Ligands and binding sites

BEZ · Benzoic acid · ligand · chains L
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains H, L, K, M
GOL · Glycerol · additive · chains K

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

Pockets

11 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	625	0.71	0.79	79	empty
2	393	0.63	0.78	48	empty
3	329	0.60	0.77	41	empty
4	80	0.45	0.81	22	empty
5	100	0.38	0.75	24	empty

Interfaces

6 interfaces between chains.

K–M · 1023 Å² buried · 9 hydrogen bonds · protein-protein
L–H · 990 Å² buried · 9 hydrogen bonds · protein-protein
H–K · 965 Å² buried · 6 hydrogen bonds · protein-protein
L–M · 953 Å² buried · 8 hydrogen bonds · protein-protein
H–M · 946 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6N35 · Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement · the same entry in another collection · chain L against L, TM-score 1.00
P0DOX7 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa light chain (P0DOX7) · a predicted model of the same protein · chain L against A, TM-score 0.83

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 6N35 · PDBe 6N35 · UniProt P0DOX7 · UniProt P0DOX5

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