MolNFT v1 · #15974 · protein
Crystal structure of human factor IX gla domain in complex of an inhibitory antibody, 10C12
1NL0 · Anti-factor IX antibody, 10C12, chain L: “Crystal structure of human factor IX gla domain in complex of an inhibitory antibody, 10C12”. X-ray diffraction, 2 ligands (CA, SO4), 6 pockets (best druggability 0.66). MolNFT v1 #15974 on…
- PDB
- 1NL0
- Type
- protein
- Length
- 474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-factor IX antibody, 10C12, chain L; Anti-factor IX antibody, 10C12, chain H; Factor…
- UniProt
- P00740
- Ligands
- CA, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anti-factor IX antibody, 10C12, chain L | protein | 213 | 8% helix, 47% strand | — |
| H | Anti-factor IX antibody, 10C12, chain H | protein | 216 | 7% helix, 53% strand | — |
| G | Factor IX | protein | 45 | 47% helix, 0% strand | P00740 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.66 | 0.75 | 62 | empty |
| 2 | 91 | 0.42 | 0.79 | 22 | empty |
| 3 | 115 | 0.42 | 0.77 | 28 | empty |
| 4 | 70 | 0.41 | 0.80 | 16 | empty |
| 5 | 61 | 0.28 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1873 Ų buried · 16 hydrogen bonds · protein-protein
- H–G · 537 Ų buried · 1 hydrogen bond · protein-protein
- L–G · 148 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 5 disulfide (carboxylation, disulfide).
Compared structures
- 1NL0 · Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody… · the same entry in another collection · chain L against L, TM-score 1.00
- P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain G against A, TM-score 0.61
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 P00740
- Elsewhere: RCSB PDB 1NL0 · PDBe 1NL0 · UniProt P00740
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