[English] 日本語
Yorodumi
- PDB-2a1d: Staphylocoagulase bound to bovine thrombin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a1d
TitleStaphylocoagulase bound to bovine thrombin
Components
  • (thrombin) x 2
  • Staphylocoagulase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / prothrombin activator / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


peptidase activator activity / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding ...peptidase activator activity / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Staphylcoagulase, helix bundle domain 1 / Staphylcoagulase, helix bundle, domain 2 / Staphylocoagulase repeat / Staphylocoagulase, N-terminal, subdomain 1 / Staphylcoagulase, N-terminal, subdomain 2 / Staphylcoagulase, N-terminal, subdomain 1 / Staphylocoagulase repeat / Staphylococcus aureus coagulase / Staphylocoagulase repeat signature. / Epsilon-Thrombin; Chain L ...Staphylcoagulase, helix bundle domain 1 / Staphylcoagulase, helix bundle, domain 2 / Staphylocoagulase repeat / Staphylocoagulase, N-terminal, subdomain 1 / Staphylcoagulase, N-terminal, subdomain 2 / Staphylcoagulase, N-terminal, subdomain 1 / Staphylocoagulase repeat / Staphylococcus aureus coagulase / Staphylocoagulase repeat signature. / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle 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. / Kringle-like fold / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures / Irregular / 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 / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Prothrombin / Staphylocoagulase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsFriedrich, R. / Panizzi, P. / Kawabata, S. / Bode, W. / Bock, P.E. / Fuentes-Prior, P.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Basis for Reduced Staphylocoagulase-mediated Bovine Prothrombin Activation
Authors: Friedrich, R. / Panizzi, P. / Kawabata, S. / Bode, W. / Bock, P.E. / Fuentes-Prior, P.
History
DepositionJun 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: thrombin
B: thrombin
D: Staphylocoagulase
E: thrombin
F: thrombin
H: Staphylocoagulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,38911
Polymers146,2136
Non-polymers1,1755
Water0
1
A: thrombin
B: thrombin
D: Staphylocoagulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8056
Polymers73,1073
Non-polymers6983
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-36 kcal/mol
Surface area28680 Å2
MethodPISA
2
E: thrombin
F: thrombin
H: Staphylocoagulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5845
Polymers73,1073
Non-polymers4772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-38 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.780, 102.540, 134.040
Angle α, β, γ (deg.)90.00, 129.14, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 4 molecules BFDH

#2: Protein thrombin / / Coagulation factor II


Mass: 29772.422 Da / Num. of mol.: 2 / Fragment: Thrombin heavy chain / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#3: Protein Staphylocoagulase


Mass: 38541.992 Da / Num. of mol.: 2 / Fragment: active fragment 1-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P17855

-
Protein/peptide / Sugars , 2 types, 3 molecules AE

#1: Protein/peptide thrombin / / Coagulation factor II


Mass: 4792.293 Da / Num. of mol.: 2 / Fragment: Thrombin light chain / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 4 molecules

#4: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / THROMBIN-SPECIFIC INHIBITOR / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / Details: CHEMICALLY SYNTHESIZED / References: D-Phe-Pro-Arg-CH2Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

-
Details

Nonpolymer detailsTHE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER ...THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER 195 IN CHAINS B AND F, 2) VIA A METHYLENE GROUP TO NE2 HIS 57 IN CHAINS B AND F.
Sequence detailsTHIS DIVERGENCE OF GLY FROM THE REPORTED SEQUENCE, PERHAPS ADDING THAT THIS VARIATION IS IRRELEVANT ...THIS DIVERGENCE OF GLY FROM THE REPORTED SEQUENCE, PERHAPS ADDING THAT THIS VARIATION IS IRRELEVANT FOR (PRO)THROMBIN BINDING, WHICH IS AN IMPORTANT POINT OF THIS ENTRY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M IMIDAZOLE, 0.2M AMMONIUM FORMATE, 12% POLYETHYLENE GLYCOL 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→55.7 Å / Num. obs: 138556 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
CNS1.1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN THROMBIN-STAPHYLOCOAGULASE COMPLEX

Resolution: 3.5→31.69 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.306 420 -RANDOM
Rwork0.233 ---
obs-21210 86.7 %-
Displacement parametersBiso mean: 59.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å29.55 Å2
2---1.04 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.5→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9558 0 76 0 9634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.075
RfactorNum. reflection% reflection
Rfree0.394 28 -
Rwork0.266 --
obs-1429 36.2 %

+
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