Research workbench

Structure of dbp in complex with human neutralizing antibody 092096

Analyse Structure of dbp in complex with human neutralizing antibody 092096 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OAO
Type: protein
Length: 3,080 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Duffy binding surface protein region II; Antibody 092096 single chain variable fragment
UniProt: B7T089
Ligands: SO4
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 8 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Duffy binding surface protein region II	protein	284	65% helix, 1% strand	B7T089
B, D, L	Antibody 092096 single chain variable fragment	protein	227	6% helix, 44% strand	—
C	Duffy binding surface protein region II	protein	288	63% helix, 1% strand	B7T089
E, K	Duffy binding surface protein region II	protein	285	64% helix, 1% strand	B7T089
F	Antibody 092096 single chain variable fragment	protein	229	6% helix, 44% strand	—
H	Antibody 092096 single chain variable fragment	protein	229	7% helix, 44% strand	—
I	Duffy binding surface protein region II	protein	287	63% helix, 1% strand	B7T089
J	Antibody 092096 single chain variable fragment	protein	228	6% helix, 44% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	122	0.72	0.92	24	empty
2	870	0.71	0.76	86	empty
3	140	0.70	0.91	26	empty
4	781	0.69	0.76	69	empty
5	316	0.68	0.83	42	empty

Interfaces

25 interfaces between chains.

E–F · 1199 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 1196 Å² buried · 15 hydrogen bonds · protein-protein
I–J · 1182 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1179 Å² buried · 17 hydrogen bonds · protein-protein
K–L · 1179 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide (disulfide).

Compared structures

6OAO · Structure of DBP in complex with human neutralizing antibody 092096 · 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
Every structure of UniProt B7T089
Elsewhere: RCSB PDB 6OAO · PDBe 6OAO · UniProt B7T089

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