3TH3

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/pdb3TH3/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: 2.70 Å
R-Value Free:
0.298 (Depositor), 0.290 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 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, M.S., Krishnaswamy, S., Esmon, C.T., Padmanabhan, K., Bajaj, S.P.

To be published.

Macromolecule Content

Total Structure Weight: 68.85 kDa
Atom Count: 4,082
Modelled Residue Count: 504
Deposited Residue Count: 601
Unique protein chains: 3

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

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 Annotations Expand
Reference Sequence LOADING

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 Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0GE Query on 0GE Download Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H] mmCIF format, chain G [auth H]	G [auth H]	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 G [auth H] Interactions & Density Focus chain G [auth H]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain F [auth L] MOL2 format, chain F [auth L] mmCIF format, chain F [auth L]	F [auth L]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain F [auth L] Interactions & Density Focus chain F [auth L]
FUC Query on FUC 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]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain H MOL2 format, chain E [auth L] MOL2 format, chain H mmCIF format, chain E [auth L] mmCIF format, chain H	E [auth L], H	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth L] Focus chain H Interactions & Density Focus chain E [auth L] Focus chain H
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth H] MOL2 format, chain I [auth H] mmCIF format, chain I [auth H]	I [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth H] Interactions & Density Focus chain I [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: 7
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000287 (0GE) Query on PRD_000287	G [auth H]	dansyl-Glu-Gly-Arg chloromethyl ketone	Peptide-like / Inhibitor		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.298 (Depositor), 0.290 (DCC)
R-Value Work: 0.228 (Depositor), 0.230 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.079	α = 90
b = 68.894	β = 91.19
c = 79.153	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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: 2018-01-24
Changes: Database references
Version 2.0: 2018-10-03
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.3: 2023-12-06
Changes: Data collection