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
Deposition Author(s): Vadivel, K., Agah, S., Cascio, D., Padmanabhan, K., Bajaj, S.P.

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+

Vadivel, K., Agah, S., Messer, A., Cascio, D., Bajaj, S.M., Krishnaswamy, S., Esmon, C.T., Padmanabhan, K., Bajaj, S.P.

To be published.

Macromolecule Content

Total Structure Weight: 69.2 kDa
Atom Count: 5,118
Modelled Residue Count: 587
Deposited Residue Count: 601
Unique protein chains: 3

Macromolecules

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(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
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth L]	Go to GlyGen: P08709-1
Sequence Annotations Expand
Reference Sequence

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(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 Annotations Expand
Reference Sequence

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(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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0GE Query on 0GE Download Ideal Coordinates CCD File SDF format, chain N [auth L] MOL2 format, chain N [auth L] mmCIF format, chain N [auth L]	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		Interactions Focus chain N [auth L] Interactions & Density Focus chain N [auth L]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L] mmCIF format, chain D [auth L]	D [auth L]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain E [auth L] MOL2 format, chain E [auth L] mmCIF format, chain E [auth L]	E [auth L]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain E [auth L] Interactions & Density Focus chain E [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain M [auth L] SDF format, chain P [auth H] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain M [auth L] MOL2 format, chain P [auth H] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain M [auth L] mmCIF format, chain P [auth H]	G [auth L] H [auth L] I [auth L] J [auth L] K [auth L] G [auth L], H [auth L], I [auth L], J [auth L], K [auth L], M [auth L], P [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain M [auth L] Focus chain P [auth H] Interactions & Density Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain M [auth L] Focus chain P [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth L] SDF format, chain R [auth H] SDF format, chain S [auth H] MOL2 format, chain O [auth L] MOL2 format, chain R [auth H] MOL2 format, chain S [auth H] mmCIF format, chain O [auth L] mmCIF format, chain R [auth H] mmCIF format, chain S [auth H]	O [auth L], R [auth H], S [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth L] Focus chain R [auth H] Focus chain S [auth H] Interactions & Density Focus chain O [auth L] Focus chain R [auth H] Focus chain S [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain L MOL2 format, chain F [auth L] MOL2 format, chain L mmCIF format, chain F [auth L] mmCIF format, chain L	F [auth L], L	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Focus chain L Interactions & Density Focus chain F [auth L] Focus chain L
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Q [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain Q [auth H]	Q [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth H] Interactions & Density Focus chain Q [auth H]

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		Interactions Focus chain N [auth L] Interactions & Density Focus chain N [auth L]

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 Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

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

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Help and Resources

3TH4

Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+

Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 8

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)