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Crystal structure and thermodynamic analysis of diagnostic Fab 106.3 complexed with bnp 5-13 (C10A) reveal basis of selective molecular recognition
Analyse Crystal structure and thermodynamic analysis of diagnostic Fab 106.3 complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E8U
- Type
- protein
- Length
- 439 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 106.3 heavy chain; Fab 106.3 light chain; Bnp peptide epitope
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab 106.3 heavy chain | protein | 213 | 8% helix, 53% strand | — |
| L | Fab 106.3 light chain | protein | 216 | 6% helix, 53% strand | — |
| P | Bnp peptide epitope | protein | 10 | 40% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.62 | 0.75 | 56 | empty |
| 2 | 72 | 0.38 | 0.78 | 18 | empty |
| 3 | 96 | 0.34 | 0.73 | 23 | empty |
| 4 | 71 | 0.33 | 0.75 | 18 | empty |
| 5 | 54 | 0.28 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1828 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 429 Ų buried · 12 hydrogen bonds · protein-protein
- L–P · 261 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3E8U · Crystal structure and thermodynamic analysis of diagnostic Fab 106.3 complexed with BNP… · the same entry in another collection · chain H against H, 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 3E8U · PDBe 3E8U
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