3ELA
Crystal structure of active site inhibited coagulation factor VIIA mutant in complex with soluble tissue factor
- PDB DOI: https://doi.org/10.2210/pdb3ELA/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus, Escherichia coli
- Mutation(s): Yes
- Deposited: 2008-09-21 Released: 2008-11-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.294
- R-Value Work: 0.233
- R-Value Observed: 0.236
This is version 1.6 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coagulation factor VIIA light chain | A [auth L] | 152 | 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 | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Coagulation factor VIIA heavy chain | B [auth H] | 254 | Homo sapiens | Mutation(s): 3 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: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Tissue factor | C [auth T] | 209 | Homo sapiens | Mutation(s): 0 Gene Names: F3 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P13726 (Homo sapiens) Explore P13726 Go to UniProtKB: P13726 | |||||
PHAROS: P13726 GTEx: ENSG00000117525 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13726 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 0Z6 Query on 0Z6 | G [auth H] | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide C25 H36 Cl N6 O3 ZKHBINZTIMXMQW-CLAROIROSA-O |  | ||
| GLC Query on GLC | D [auth L] | alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N |  | ||
| FUC Query on FUC | E [auth L] | alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N |  | ||
| CA Query on CA | F [auth H] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000369 (0Z6) Query on PRD_000369 | G [auth H] | D-Phe-Phe-Arg Chloromethylketone | Peptide-like / Inhibitor | | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.294
- R-Value Work: 0.233
- R-Value Observed: 0.236
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 78.361 | α = 90 |
| b = 68.558 | β = 90.22 |
| c = 78.817 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345 | data collection |
| CCP4 | model building |
| MOLREP | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| CCP4 | phasing |
Entry History
Deposition Data
- Released Date: 2008-11-04 Deposition Author(s): Bjelke, J.R., Fodje, M., Svensson, L.A.
Revision History (Full details and data files)
- Version 1.0: 2008-11-04
Type: Initial release - Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance - Version 1.2: 2013-02-27
Changes: Other - Version 1.3: 2017-10-25
Changes: Data collection, Refinement description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2021-11-10
Changes: Database references, Structure summary - Version 1.6: 2023-11-01
Changes: Data collection, Refinement description
