Download MendeleyCrystal Structure of a Factor VIIa complex
Mayweg, A., Roever, S., Rudolph, M.G.To be published.
5PB4
human factor VIIa in complex with 1-[[3-[5-hydroxy-3-methyl-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]-3-phenylurea at 2.43A
- PDB DOI: https://doi.org/10.2210/pdb5PB4/pdb
- Deposition Group: G_1002016 ExploreG_1002016
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2016-11-16 Released: 2017-06-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.43 Å
- R-Value Free: 0.230
- R-Value Work: 0.200
- R-Value Observed: 0.201
This is version 1.3 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coagulation factor VII light chain | 64 | Homo sapiens | Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709 | |||||
PHAROS: P08709 GTEx: ENSG00000057593 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P08709 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coagulation factor VII heavy chain | B [auth C] | 254 | Homo sapiens | Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709 | |||||
PHAROS: P08709 GTEx: ENSG00000057593 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P08709 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 9RS Query on 9RS | E [auth C] | N-({3-[5-hydroxy-3-methyl-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)-1H-pyrazol-1-yl]phenyl}methyl)-N'-phenylurea C25 H22 N6 O2 NMKKTNKAENJFOY-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | I [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CA Query on CA | F [auth C] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | G [auth C], H [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.43 Å
- R-Value Free: 0.230
- R-Value Work: 0.200
- R-Value Observed: 0.201
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 95.345 | α = 90 |
| b = 95.345 | β = 90 |
| c = 117.608 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| SADABS | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2017-06-21 Deposition Author(s): Stihle, M., Mayweg, A., Roever, S., Rudolph, M.G.
Revision History (Full details and data files)
- Version 1.0: 2017-06-21
Type: Initial release - Version 1.1: 2018-02-21
Changes: Structure summary - Version 1.2: 2021-11-17
Changes: Database references, Derived calculations, Structure summary - Version 1.3: 2024-04-03
Changes: Data collection, Refinement description
