Research workbench
Crystal structure of CA(II)-bound gla domain of factor IX complexed with binding protein
Analyse Crystal structure of CA(II)-bound gla domain of factor IX complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J35
- Type
- protein
- Length
- 298 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor IX-binding protein a chain; Coagulation factor IX-binding protein B…
- EC
- 3.4.21.22
- UniProt
- P23806, P23807, P00741
- Ligands
- CA
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor IX-binding protein a chain | protein | 129 | 22% helix, 29% strand | P23806 |
| B | Coagulation factor IX-binding protein B chain | protein | 123 | 19% helix, 33% strand | P23807 |
| C | Coagulation factor IX (EC 3.4.21.22) | protein | 46 | 57% helix, 0% strand | P00741 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.73 | 0.85 | 37 | empty |
| 2 | 75 | 0.35 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1878 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 639 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 531 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 8 disulfide (carboxylation, disulfide).
Compared structures
- 1J35 · Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein · the same entry in another collection · chain C against C, TM-score 1.00
- P23807 · AlphaFold monomer V2.0 prediction for snaclec coagulation factor IX/FACTOR X-binding… · a predicted model of the same protein · chain B against A, TM-score 0.92
- P23806 · AlphaFold monomer V2.0 prediction for snaclec coagulation factor IX/FACTOR X-binding… · a predicted model of the same protein · chain A against A, TM-score 0.78
- P00741 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00741) · a predicted model of the same protein · chain C against A, TM-score 0.62
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 P23806
- Every structure of UniProt P23807
- Every structure of UniProt P00741
- Elsewhere: RCSB PDB 1J35 · PDBe 1J35 · UniProt P23806 · UniProt P23807 · UniProt P00741
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