Research workbench
Crystal structure of FAB399 in complex with NPNA3 peptide from circumsporozoite protein
Analyse Crystal structure of FAB399 in complex with NPNA3 peptide from circumsporozoite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WFZ
- Type
- protein
- Length
- 890 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAB399 heavy chain; FAB399 light chain; NPNA3 peptide
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAB399 heavy chain | protein | 216 | 10% helix, 52% strand | — |
| B | FAB399 light chain | protein | 219 | 5% helix, 50% strand | — |
| C, P | NPNA3 peptide | protein | 11 | 27% helix, 0% strand | — |
| H | FAB399 heavy chain | protein | 215 | 10% helix, 52% strand | — |
| L | FAB399 light chain | protein | 218 | 5% helix, 50% strand | — |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.65 | 0.95 | 16 | empty |
| 2 | 454 | 0.58 | 0.74 | 57 | empty |
| 3 | 458 | 0.57 | 0.74 | 52 | empty |
| 4 | 275 | 0.57 | 0.78 | 46 | empty |
| 5 | 61 | 0.46 | 0.84 | 23 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1760 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1736 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 544 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 382 Ų buried · 6 hydrogen bonds · protein-protein
- H–P · 382 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6WFZ · Crystal structure of Fab399 in complex with NPNA3 peptide from circumsporozoite protein · 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
- Elsewhere: RCSB PDB 6WFZ · PDBe 6WFZ
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