[English] 日本語
Yorodumi
- PDB-1ygc: Short Factor VIIa with a small molecule inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ygc
TitleShort Factor VIIa with a small molecule inhibitor
Components(Coagulation factor ...) x 2
KeywordsHYDROLASE / inverted oxy-anion hole
Function / homology
Function and homology information


coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-905 / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOlivero, A.G. / Eigenbrot, C. / Goldsmith, R. / Robarge, K. / Artis, D.R. / Flygare, J. / Rawson, T. / Refino, C. / Bunting, S. / Kirchhofer, D.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo.
Authors: Olivero, A.G. / Eigenbrot, C. / Goldsmith, R. / Robarge, K. / Artis, D.R. / Flygare, J. / Rawson, T. / Sutherlin, D.P. / Kadkhodayan, S. / Beresini, M. / Elliott, L.O. / DeGuzman, G.G. / ...Authors: Olivero, A.G. / Eigenbrot, C. / Goldsmith, R. / Robarge, K. / Artis, D.R. / Flygare, J. / Rawson, T. / Sutherlin, D.P. / Kadkhodayan, S. / Beresini, M. / Elliott, L.O. / DeGuzman, G.G. / Banner, D.W. / Ultsch, M. / Marzec, U. / Hanson, S.R. / Refino, C. / Bunting, S. / Kirchhofer, D.
History
DepositionJan 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Coagulation factor VII
L: Coagulation factor VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,27312
Polymers34,9752
Non-polymers1,29810
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-119 kcal/mol
Surface area13590 Å2
MethodPISA
2
H: Coagulation factor VII
L: Coagulation factor VII
hetero molecules

H: Coagulation factor VII
L: Coagulation factor VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,54624
Polymers69,9504
Non-polymers2,59620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9680 Å2
ΔGint-252 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.220, 95.220, 116.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11H-538-

CA

-
Components

-
Coagulation factor ... , 2 types, 2 molecules HL

#1: Protein Coagulation factor VII / Serum prothrombin conversion accelerator / SPCA / Proconvertin / Eptacog alfa


Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: heavy chain (residues 213-466)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Plasmid: gp67ssFVII / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five / References: UniProt: P08709, coagulation factor VIIa
#2: Protein Coagulation factor VII / Serum prothrombin conversion accelerator / SPCA / Proconvertin / Eptacog alfa


Mass: 6871.753 Da / Num. of mol.: 1
Fragment: light chain, del 1-149 from full length (residues 150-212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Plasmid: gp67ssFVII / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five / References: UniProt: P08709

-
Non-polymers , 4 types, 270 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-905 / (R)-4-[2-(3-AMINO-BENZENESULFONYLAMINO)-1-(3,5-DIETHOXY-2-FLUOROPHENYL)-2-OXO-ETHYLAMINO]-2-HYDROXY-BENZAMIDINE


Mass: 545.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28FN5O6S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, glycerol, PEG 400, Calcium ion, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 36852 / Num. obs: 34943 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.5 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.3

-
Processing

Software
NameVersionClassification
CNX2000.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2203986.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 878 2.5 %RANDOM
Rwork0.188 ---
all0.189 34943 --
obs0.189 34943 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.7391 Å2 / ksol: 0.359589 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2---1.32 Å20 Å2
3---2.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 75 260 2703
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it2.273
X-RAY DIFFRACTIONc_mcangle_it2.864
X-RAY DIFFRACTIONc_scbond_it4.224
X-RAY DIFFRACTIONc_scangle_it5.356
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 49 0.9 %
Rwork0.201 5598 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARWAT.PROTOPWAT.PRO
X-RAY DIFFRACTION3PARAM.CALCIUMTOP.CALCIUM
X-RAY DIFFRACTION4905.PAR905.TOP
X-RAY DIFFRACTION5PARAM.SO4TOP.SO4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more