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 v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.497
- Source
- Homo sapiens; Plasmodium vivax
- 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 · resolution 3.497 · 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.
| Volume (ų) | 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 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1196 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 1182 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1179 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 1179 Ų 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
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