[English] 日本語
Yorodumi
- PDB-7kme: CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2711. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kme
TitleCRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2711.
Components
  • HIRUGEN
  • SEL2711
  • THROMBIN H-CHAIN
  • THROMBIN L-CHAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SELECTIDE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / cytolysis by host of symbiont cells / thrombin / regulation of blood coagulation / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / cytolysis by host of symbiont cells / thrombin / regulation of blood coagulation / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / negative regulation of blood coagulation / blood coagulation, common pathway / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / Peptide ligand-binding receptors / positive regulation of receptor signaling pathway via JAK-STAT / fibrinolysis / positive regulation of release of sequestered calcium ion into cytosol / Intrinsic Pathway of Fibrin Clot Formation / zymogen activation / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade / lipopolysaccharide binding / acute-phase response / Cell surface interactions at the vascular wall / serine-type endopeptidase complex / negative regulation of proteolysis / growth factor activity / positive regulation of protein localization to nucleus / response to wounding / platelet activation / Golgi lumen / positive regulation of reactive oxygen species metabolic process / G alpha (q) signalling events / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / positive regulation of phosphatidylinositol 3-kinase signaling / heparin binding / regulation of cell shape / positive regulation of cell growth / collagen-containing extracellular matrix / blood microparticle / antimicrobial humoral immune response mediated by antimicrobial peptide / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / signaling receptor binding / proteolysis / serine-type endopeptidase activity / endoplasmic reticulum lumen / calcium ion binding / positive regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Prothrombin/thrombin / Thrombin light chain domain superfamily / Thrombin light chain / Thrombin light chain / Kringle domain / Kringle superfamily / Kringle, conserved site / Kringle domain signature. / Kringle / Kringle domain profile. ...Prothrombin/thrombin / Thrombin light chain domain superfamily / Thrombin light chain / Thrombin light chain / Kringle domain / Kringle superfamily / Kringle, conserved site / Kringle domain signature. / Kringle / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / 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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / 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
N-{(2S)-2-[(N-acetyl-4-carbamimidoyl-L-phenylalanyl)amino]-2-cyclohexylacetyl}-3-(1-methylpyridinium-3-yl)- L-alanyl-D-leucyl-L-prolinamide / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMochalkin, I. / Tulinsky, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structures of thrombin retro-inhibited with SEL2711 and SEL2770 as they relate to factor Xa binding.
Authors: Mochalkin, I. / Tulinsky, A.
History
DepositionFeb 26, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 9, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Remark 285THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: THROMBIN L-CHAIN
H: THROMBIN H-CHAIN
I: HIRUGEN
J: SEL2711
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0306
Polymers35,9844
Non-polymers462
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.050, 71.820, 73.450
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-481-

HOH

-
Components

-
Protein/peptide , 3 types, 3 molecules LIJ

#1: Protein/peptide THROMBIN L-CHAIN / E.C.3.4.21.5


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide HIRUGEN


Mass: 1363.399 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Protein/peptide SEL2711


Type: Peptide-like / Class: Inhibitor / Mass: 743.939 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-{(2S)-2-[(N-acetyl-4-carbamimidoyl-L-phenylalanyl)amino]-2-cyclohexylacetyl}-3-(1-methylpyridinium-3-yl)- L-alanyl-D-leucyl-L-prolinamide

-
Protein , 1 types, 1 molecules H

#2: Protein THROMBIN H-CHAIN / E.C.3.4.21.5


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin

-
Non-polymers , 2 types, 132 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTHROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 ...THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN INDICATOR *I* IS USED FOR HIRUGEN 53 - 64 WITH SULFATO-TYR AT 63.
Nonpolymer detailsOCCUPIES THE SPECIFICITY SITE OF THROMBIN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growpH: 7.3 / Details: pH 7.30
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
228 %PEG80001reservoir
30.1 Msodium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Feb 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 17688 / % possible obs: 78 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.1→2.3 Å / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 3.2 / % possible all: 52
Reflection
*PLUS
Num. measured all: 28464
Reflection shell
*PLUS
% possible obs: 52 %

-
Processing

SoftwareName: PROFFT / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HAH
Resolution: 2.1→9 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.165 --
obs-14194 78 %
Refinement stepCycle: LAST / Resolution: 2.1→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 2 130 2465
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.011
X-RAY DIFFRACTIONp_angle_d0.030.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.047
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it11
X-RAY DIFFRACTIONp_mcangle_it1.51.7
X-RAY DIFFRACTIONp_scbond_it22.5
X-RAY DIFFRACTIONp_scangle_it33.6
X-RAY DIFFRACTIONp_plane_restr0.040.034
X-RAY DIFFRACTIONp_chiral_restr0.150.17
X-RAY DIFFRACTIONp_singtor_nbd0.60.22
X-RAY DIFFRACTIONp_multtor_nbd0.60.25
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.60.25
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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://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