3TH4
Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+
- PDB DOI: https://doi.org/10.2210/pdb3TH4/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2011-08-18 Released: 2012-08-22 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.235 
- R-Value Work: 0.204 
- R-Value Observed: 0.206 
This is version 1.5 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 light chain | A [auth L] | 142 | 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 heavy chain | 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 | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Tissue factor | C [auth T] | 205 | 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 | |
0GE Query on 0GE | N [auth L] | N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-alpha-glutamyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]glycinamide C26 H38 Cl N7 O7 S AKFRXQNHCCSRJN-IRFCIJBXSA-N | |||
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 | |||
CA Query on CA | G [auth L] H [auth L] I [auth L] J [auth L] K [auth L] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | O [auth L], R [auth H], S [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
MG Query on MG | F [auth L], L | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
NA Query on NA | Q [auth H] | SODIUM ION Na FKNQFGJONOIPTF-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 |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 8 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_000287 (0GE) Query on PRD_000287 | N [auth L] | dansyl-Glu-Gly-Arg chloromethyl ketone | Peptide-like / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.235 
- R-Value Work: 0.204 
- R-Value Observed: 0.206 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 69.919 | α = 90 |
b = 81.23 | β = 90 |
c = 126.534 | γ = 90 |
Software Name | Purpose |
---|---|
ADSC | data collection |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-08-22  Deposition Author(s): Vadivel, K., Agah, S., Cascio, D., Padmanabhan, K., Bajaj, S.P.
Revision History (Full details and data files)
- Version 1.0: 2012-08-22
Type: Initial release - Version 1.1: 2012-12-12
Changes: Other - Version 1.2: 2015-04-08
Changes: Other - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary - Version 1.4: 2023-09-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary - Version 1.5: 2023-12-06
Changes: Data collection