MolNFT v1 · #77598 · protein

Crystal structure of anti-HIV llama vhh antibody A12 in complex with C186 GP120

3RJQ: “Crystal structure of anti-HIV llama vhh antibody A12 in complex with C186 GP120”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.62). MolNFT v1 #77598 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3RJQ
Type: protein
Length: 419 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C186 GP120; Llama vhh A12
Ligands: NAG
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C186 GP120	protein	292	18% helix, 37% strand	—
B	Llama vhh A12	protein	127	2% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.62	0.88	21	NAG
2	233	0.52	0.76	31	empty
3	56	0.47	0.85	19	empty
4	80	0.33	0.74	19	empty
5	51	0.32	0.77	12	empty

Interfaces

1 interface between chains.

A–B · 928 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 7 disulfide (N-glycosylation, disulfide).

Compared structures

3RJQ · Crystal structure of anti-HIV llama VHH antibody A12 in complex with C186 gp120 · the same entry in another collection · chain A against A, 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 3RJQ · PDBe 3RJQ

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