Research workbench
Crystal structure of glu-gly-arg-chloromethyl ketone-factor VIIA/SOLUBLE tissue factor complex
Analyse Crystal structure of glu-gly-arg-chloromethyl ketone-factor VIIA/SOLUBLE tissue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B8O
- Type
- protein
- Length
- 587 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII light chain; Coagulation factor VII heavy chain; Tissue factor
- EC
- 3.4.21.21
- UniProt
- P08709, P13726
- Ligands
- 0GJ, GLC, FUC, CA, MG, ZN, NA, CL
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor VII light chain | protein | 142 | 25% helix, 17% strand | P08709 |
| H | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 254 | 11% helix, 33% strand | P08709 |
| T | Tissue factor | protein | 191 | 8% helix, 42% strand | P13726 |
Ligands and binding sites
- 0GJ · L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide · ligand · chains H
- GLC · alpha-D-glucopyranose · sugar · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L, T
- CA · Calcium ion · metal · 6 copies · chains L, H
- MG · Magnesium ion · metal · 2 copies · chains L
- ZN · Zinc ion · metal · 2 copies · chains H
- NA · Sodium ion · metal · chains H
- CL · Chloride ion · ion · 3 copies · chains H, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.65 | 0.80 | 46 | empty |
| 2 | 95 | 0.49 | 0.81 | 18 | empty |
| 3 | 150 | 0.48 | 0.78 | 26 | empty |
| 4 | 54 | 0.46 | 0.85 | 17 | empty |
| 5 | 67 | 0.46 | 0.83 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–T · 1329 Ų buried · 8 hydrogen bonds · protein-protein
- L–H · 969 Ų buried · 13 hydrogen bonds · protein-protein
- H–T · 616 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 modified, 2 glycan (disulfide, carboxylation, O-glycosylation).
Compared structures
- 2B8O · Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor VIIa/Soluble Tissue Factor… · the same entry in another collection · chain L against L, TM-score 1.00
- P13726 · AlphaFold monomer V2.0 prediction for tissue factor (P13726) · a predicted model of the same protein · chain T against A, TM-score 0.98
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain H against A, TM-score 0.97
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 P08709
- Every structure of UniProt P13726
- Elsewhere: RCSB PDB 2B8O · PDBe 2B8O · UniProt P08709 · UniProt P13726
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