MolNFT v1 · #167134 · protein

Crystal structure of anti-HIV-1 antibody DH815 bound to GP120 V2 peptide

6VBP · DH815 light chain: “Crystal structure of anti-HIV-1 antibody DH815 bound to GP120 V2 peptide”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.78). MolNFT v1 #167134 on GenesisL1: 3D structure, binding sites and…

PDB: 6VBP
Type: protein
Length: 1,790 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DH815 light chain; DH815 heavy chain; Envelope glycoprotein GP160
UniProt: I2E6B7
Ligands: CL
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 10 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	DH815 light chain	protein	218	6% helix, 51% strand	—
H	DH815 heavy chain	protein	214	7% helix, 53% strand	—
B, D, I	DH815 light chain	protein	219	6% helix, 51% strand	—
A	DH815 heavy chain	protein	213	7% helix, 54% strand	—
C	DH815 heavy chain	protein	221	8% helix, 51% strand	—
F	Envelope glycoprotein GP160	protein	14	0% helix, 0% strand	I2E6B7
E	Envelope glycoprotein GP160	protein	13	0% helix, 0% strand	I2E6B7
G	Envelope glycoprotein GP160	protein	14	0% helix, 0% strand	I2E6B7
J	DH815 heavy chain	protein	214	8% helix, 52% strand	—
K	Envelope glycoprotein GP160	protein	12	0% helix, 0% strand	I2E6B7

Ligands and binding sites

CL · Chloride ion · ion · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1036	0.78	0.80	116	empty
2	136	0.61	0.85	26	empty
3	255	0.55	0.77	28	empty
4	228	0.54	0.77	29	empty
5	216	0.52	0.77	33	empty

Interfaces

17 interfaces between chains.

D–C · 1843 Å² buried · 11 hydrogen bonds · protein-protein
I–J · 1832 Å² buried · 11 hydrogen bonds · protein-protein
B–A · 1754 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1740 Å² buried · 12 hydrogen bonds · protein-protein
D–I · 1331 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

6VBP · Crystal structure of anti-HIV-1 antibody DH815 bound to gp120 V2 peptide · 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 I2E6B7
Elsewhere: RCSB PDB 6VBP · PDBe 6VBP · UniProt I2E6B7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.