MolNFT v1 · #157545 · protein

Anti-HIV-1 Fab 2G12 + MAN9 re-refinement

6N2X · Fab 2G12 light chain: “Anti-HIV-1 Fab 2G12 + MAN9 re-refinement”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 12 pockets (best druggability 0.76). MolNFT v1 #157545 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N2X
Type: protein
Length: 868 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: MAN, NAG, BMA
Pockets: 12 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, K	Fab 2G12 light chain	protein	213	6% helix, 53% strand	P0DOX7
H	Fab 2G12 heavy chain	protein	218	7% helix, 52% strand	P0DOX5
M	Fab 2G12 heavy chain	protein	224	7% helix, 50% strand	P0DOX5

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 16 copies · chains L, H, K, M
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies
BMA · beta-D-mannopyranose · sugar · 2 copies · chains H, M

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	949	0.76	0.78	97	empty
2	357	0.63	0.79	48	empty
3	283	0.58	0.78	38	empty
4	96	0.53	0.84	24	empty
5	177	0.44	0.74	30	empty

Interfaces

6 interfaces between chains.

K–M · 1024 Å² buried · 9 hydrogen bonds · protein-protein
L–H · 1011 Å² buried · 10 hydrogen bonds · protein-protein
L–M · 1001 Å² buried · 5 hydrogen bonds · protein-protein
H–M · 951 Å² buried · 12 hydrogen bonds · protein-protein
H–K · 833 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6N2X · Anti-HIV-1 Fab 2G12 + Man9 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 0.84

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 6N2X · PDBe 6N2X · UniProt P0DOX7 · UniProt P0DOX5

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