4IBL
Rubidium Sites in Blood Coagulation Factor VIIa
- PDB DOI: https://doi.org/10.2210/pdb4IBL/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2012-12-08 Released: 2014-04-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.215 
- R-Value Work: 0.175 
- R-Value Observed: 0.179 
This is version 1.4 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 VII | A [auth L] | 152 | Homo sapiens | Mutation(s): 0  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 VII | B [auth H] | 254 | Homo sapiens | Mutation(s): 0  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] | 219 | Homo sapiens | Mutation(s): 0  | |
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 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BGC Query on BGC | D [auth L] | beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N | |||
FUC Query on FUC | E [auth L] | alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N | |||
BEN Query on BEN | P [auth H] | BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N | |||
RB Query on RB | H [auth L] J [auth L] N [auth L] O [auth L] S [auth H] | RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N | |||
CA Query on CA | G [auth L], K [auth L], M [auth L], Q [auth H] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | R [auth H], U [auth H], V [auth H], W [auth T] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
MG Query on MG | F [auth L], I [auth L], L | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
CGU Query on CGU | A [auth L] | L-PEPTIDE LINKING | C6 H9 N O6 | GLU |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.215 
- R-Value Work: 0.175 
- R-Value Observed: 0.179 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 69.9 | α = 90 |
b = 81.06 | β = 90 |
c = 126.42 | γ = 90 |
Software Name | Purpose |
---|---|
ADSC | data collection |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-04-16  Deposition Author(s): Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Bajaj, S.P.
Revision History (Full details and data files)
- Version 1.0: 2014-04-16
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2021-06-09
Changes: Database references, Structure summary - Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description - Version 1.4: 2023-12-06
Changes: Data collection