Research workbench
Crystal structure of PFS25 in complex with the transmission blocking antibody 1262
Analyse Crystal structure of PFS25 in complex with the transmission blocking antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B0H
- Type
- protein
- Length
- 1,199 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PFS25; 1262 antibody, heavy chain; 1262 antibody, light chain
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | PFS25 | protein | 168 | 4% helix, 46% strand | — |
| J | PFS25 | protein | 162 | 4% helix, 48% strand | — |
| B | 1262 antibody, heavy chain | protein | 221 | 10% helix, 53% strand | — |
| D | 1262 antibody, heavy chain | protein | 222 | 10% helix, 53% strand | — |
| A, C | 1262 antibody, light chain | protein | 213 | 5% helix, 52% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains J, B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.82 | 0.88 | 72 | EDO |
| 2 | 206 | 0.68 | 0.86 | 42 | empty |
| 3 | 339 | 0.65 | 0.80 | 45 | empty |
| 4 | 147 | 0.64 | 0.86 | 29 | empty |
| 5 | 158 | 0.52 | 0.79 | 41 | empty |
Interfaces
12 interfaces between chains.
- D–C · 2003 Ų buried · 19 hydrogen bonds · protein-protein
- B–A · 1999 Ų buried · 17 hydrogen bonds · protein-protein
- I–D · 570 Ų buried · 11 hydrogen bonds · protein-protein
- J–B · 553 Ų buried · 10 hydrogen bonds · protein-protein
- I–C · 429 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 6B0H · Crystal structure of Pfs25 in complex with the transmission blocking antibody 1262 · the same entry in another collection · chain I against I, 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
- Elsewhere: RCSB PDB 6B0H · PDBe 6B0H
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