Research workbench
Crystal structure of habu IX-bp at pH 6.5
Analyse Crystal structure of habu IX-bp at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X2T
- Type
- protein
- Length
- 504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor IX/X-binding protein a chain; Coagulation factor IX/FACTOR X-binding…
- UniProt
- Q7LZ71, P23807
- Ligands
- CA
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Coagulation factor IX/X-binding protein a chain | protein | 129 | 22% helix, 29% strand | Q7LZ71 |
| B, D | Coagulation factor IX/FACTOR X-binding protein B chain | protein | 123 | 20% helix, 33% strand | P23807 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.66 | 0.77 | 65 | empty |
| 2 | 245 | 0.54 | 0.77 | 28 | empty |
| 3 | 135 | 0.45 | 0.77 | 29 | 1PE |
Interfaces
5 interfaces between chains.
- A–B · 1883 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1857 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 237 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 216 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 172 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1X2T · Crystal Structure of Habu IX-bp at pH 6.5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q7LZ71 · AlphaFold monomer V2.0 prediction for snaclec coagulation factor IX- binding protein… · a predicted model of the same protein · chain A against A, TM-score 0.94
- 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 0.93
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 Q7LZ71
- Every structure of UniProt P23807
- Elsewhere: RCSB PDB 1X2T · PDBe 1X2T · UniProt Q7LZ71 · UniProt P23807
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