MolNFT v1 · #77791 · protein

Crystal structure of Fab from 3BNC60, highly potent anti-HIV antibody

3RPI · Light chain from highly potent anti-HIV neutralizing…: “Crystal structure of Fab from 3BNC60, highly potent anti-HIV antibody”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.77). MolNFT v1 #77791 on GenesisL1: 3D…

PDB: 3RPI
Type: protein
Length: 830 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain from highly potent anti-HIV neutralizing antibody; Heavy chain from highly…
Ligands: NAG
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, B	Light chain from highly potent anti-HIV neutralizing antibody	protein	203	6% helix, 51% strand	—
H, A	Heavy chain from highly potent anti-HIV neutralizing antibody	protein	212	8% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1136	0.77	0.79	114	empty
2	149	0.48	0.78	33	empty
3	89	0.38	0.77	21	empty

Interfaces

6 interfaces between chains.

A–B · 1645 Å² buried · 16 hydrogen bonds · protein-protein
L–H · 1639 Å² buried · 15 hydrogen bonds · protein-protein
L–A · 184 Å² buried · 2 hydrogen bonds · protein-protein
H–B · 180 Å² buried · 2 hydrogen bonds · protein-protein
H–A · 138 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3RPI · Crystal Structure of Fab from 3BNC60, Highly Potent anti-HIV Antibody · 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 3RPI · PDBe 3RPI

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