MolNFT v1 · #64912 · protein

Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 peptide W2RW020

3GHB · Fab 447-52D, light chain: “Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 peptide W2RW020”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.69). MolNFT v1 #64912 on GenesisL1: 3D structure, binding…

PDB: 3GHB
Type: protein
Length: 921 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 447-52D, light chain; Fab 447-52D, heavy chain; Envelope glycoprotein
UniProt: P88213
Ligands: SO4
Pockets: 12 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Fab 447-52D, light chain	protein	216	8% helix, 49% strand	—
H, I	Fab 447-52D, heavy chain	protein	235	9% helix, 52% strand	—
P	Envelope glycoprotein	protein	10	0% helix, 30% strand	P88213
Q	Envelope glycoprotein	protein	9	0% helix, 44% strand	P88213

Ligands and binding sites

SO4 · Sulfate ion · ion · chains L, H, M, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.69	0.96	21	empty
2	812	0.68	0.75	90	empty
3	443	0.59	0.75	55	empty
4	219	0.52	0.77	29	empty
5	210	0.50	0.76	26	empty

Interfaces

10 interfaces between chains.

M–I · 1828 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1801 Å² buried · 12 hydrogen bonds · protein-protein
H–I · 520 Å² buried · 11 hydrogen bonds · protein-protein
H–P · 497 Å² buried · 8 hydrogen bonds · protein-protein
I–Q · 464 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

3GHB · Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 peptide W2RW020 · 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
Every structure of UniProt P88213
Elsewhere: RCSB PDB 3GHB · PDBe 3GHB · UniProt P88213

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