MolNFT v1 · #145762 · protein

Anti-HIV-1 Fab 2G12 in complex with glycopeptide 10F5

6CXL · Anti-HIV-1 Fab 2G12 light chain: “Anti-HIV-1 Fab 2G12 in complex with glycopeptide 10F5”. X-ray diffraction, 2 ligands (MAN, BMA), 10 pockets (best druggability 0.71). MolNFT v1 #145762 on GenesisL1: 3D structure, binding sites and…

PDB: 6CXL
Type: protein
Length: 864 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-HIV-1 Fab 2G12 light chain; Anti-HIV-1 Fab 2G12 heavy chain
Ligands: MAN, BMA
Pockets: 10 · best druggability 0.71

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, K	Anti-HIV-1 Fab 2G12 light chain	protein	213	5% helix, 52% strand	—
H	Anti-HIV-1 Fab 2G12 heavy chain	protein	218	6% helix, 51% strand	—
M	Anti-HIV-1 Fab 2G12 heavy chain	protein	220	8% helix, 51% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 16 copies · chains L, H, K, M
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

10 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	676	0.71	0.78	57	empty
2	436	0.67	0.79	59	empty
3	297	0.60	0.79	39	empty
4	103	0.53	0.83	25	empty
5	206	0.49	0.75	34	empty

Interfaces

6 interfaces between chains.

L–M · 1041 Å² buried · 5 hydrogen bonds · protein-protein
K–M · 1025 Å² buried · 10 hydrogen bonds · protein-protein
L–H · 1023 Å² buried · 8 hydrogen bonds · protein-protein
H–M · 969 Å² buried · 13 hydrogen bonds · protein-protein
H–K · 906 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6CXL · anti-HIV-1 Fab 2G12 in complex with glycopeptide 10F5 · 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
Elsewhere: RCSB PDB 6CXL · PDBe 6CXL

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