Research workbench
Crystal structure of the Fab fragment of an anti-factor IX antibody 10C12
Analyse Crystal structure of the Fab fragment of an anti-factor IX antibody 10C12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D69
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-factor IX antibody, 10C12
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Anti-factor IX antibody, 10C12 | protein | 211 | 7% helix, 45% strand | — |
| H, B | Anti-factor IX antibody, 10C12 | protein | 218 | 4% helix, 44% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.82 | 0.83 | 87 | empty |
| 2 | 848 | 0.70 | 0.76 | 68 | empty |
| 3 | 632 | 0.68 | 0.77 | 52 | empty |
| 4 | 139 | 0.46 | 0.77 | 22 | empty |
| 5 | 79 | 0.39 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1852 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1846 Ų buried · 18 hydrogen bonds · protein-protein
- L–B · 233 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 233 Ų buried · 5 hydrogen bonds · protein-protein
- H–B · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3D69 · Crystal Structure of the Fab Fragment of an Anti-Factor IX Antibody 10C12 · the same entry in another collection · chain L against L, 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 3D69 · PDBe 3D69
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