MolNFT v1 · #105658 · protein

Crystal structure of HIV neutralizing antibody 2G12 in complex with a bacterial oligosaccharide analog of mammalian oligomanose

4RBP · Fab 2G12 light chain: “Crystal structure of HIV neutralizing antibody 2G12 in complex with a bacterial oligosaccharide analog of…”. X-ray diffraction, 2 ligands (MAN, KDO), 9 pockets (best druggability 0.76). MolNFT v1 #105658 on…

PDB: 4RBP
Type: protein
Length: 870 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 2G12 light chain; Fab 2G12 heavy chain
Ligands: MAN, KDO
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, K	Fab 2G12 light chain	protein	213	6% helix, 53% strand	—
H	Fab 2G12 heavy chain	protein	220	7% helix, 52% strand	—
M	Fab 2G12 heavy chain	protein	224	9% helix, 52% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 10 copies · chains H, L, M, K
KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies
GOL · Glycerol · additive · 8 copies · chains L, M, H, K

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

Pockets

9 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	1033	0.76	0.78	107	GOL
2	664	0.67	0.76	52	empty
3	572	0.62	0.74	48	empty
4	194	0.52	0.78	25	empty
5	153	0.43	0.74	28	empty

Interfaces

6 interfaces between chains.

L–M · 1083 Å² buried · 7 hydrogen bonds · protein-protein
H–M · 993 Å² buried · 13 hydrogen bonds · protein-protein
K–M · 985 Å² buried · 12 hydrogen bonds · protein-protein
L–H · 928 Å² buried · 11 hydrogen bonds · protein-protein
H–K · 914 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4RBP · Crystal structure of HIV neutralizing antibody 2G12 in complex with a bacterial… · the same entry in another collection · chain H against H, 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 4RBP · PDBe 4RBP

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