Research workbench
Crystal structure of human factor IX gla domain in complex of an inhibitory antibody, 10C12
Analyse Crystal structure of human factor IX gla domain in complex of an inhibitory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.