Research workbench
Structure of dbp in complex with human neutralizing antibody 053054
Analyse Structure of dbp in complex with human neutralizing antibody 053054 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OAN
- Type
- protein
- Length
- 959 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Duffy binding surface protein region II; Antibody 053054 single chain variable fragment
- UniProt
- B7T089
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Duffy binding surface protein region II | protein | 254 | 66% helix, 1% strand | B7T089 |
| B | Antibody 053054 single chain variable fragment | protein | 229 | 8% helix, 48% strand | — |
| C | Duffy binding surface protein region II | protein | 248 | 66% helix, 1% strand | B7T089 |
| D | Antibody 053054 single chain variable fragment | protein | 228 | 7% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.70 | 0.94 | 23 | empty |
| 2 | 55 | 0.59 | 0.91 | 16 | empty |
| 3 | 281 | 0.58 | 0.78 | 34 | empty |
| 4 | 267 | 0.58 | 0.78 | 33 | empty |
| 5 | 95 | 0.42 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 937 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 926 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 735 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6OAN · Structure of DBP in complex with human neutralizing antibody 053054 · 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 6OAN · PDBe 6OAN · UniProt B7T089
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