[English] 日本語
Yorodumi
- PDB-1ucy: THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ucy
TitleTHROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN
Components
  • (THROMBIN) x 4
  • FIBRINOPEPTIDE A-ALPHA
KeywordsCOMPLEX (SERINE PROTEASE/COAGULATION) / COMPLEX (SERINE PROTEASE-COAGULATION) / SERINE / PROTEASE / THROMBIN / COMPLEX (SERINE PROTEASE-COAGULATION) complex
Function / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / blood coagulation / collagen-containing extracellular matrix / adaptive immune response / serine-type endopeptidase activity ...fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / blood coagulation / collagen-containing extracellular matrix / adaptive immune response / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Prothrombin / Fibrinogen alpha chain / Fibrinogen alpha chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMartin, P. / Edwards, B.
CitationJournal: Biochemistry / Year: 1996
Title: Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues.
Authors: Martin, P.D. / Malkowski, M.G. / DiMaio, J. / Konishi, Y. / Ni, F. / Edwards, B.F.
History
DepositionAug 30, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: THROMBIN
H: THROMBIN
E: THROMBIN
F: FIBRINOPEPTIDE A-ALPHA
J: THROMBIN
K: THROMBIN
G: FIBRINOPEPTIDE A-ALPHA
M: THROMBIN
N: THROMBIN
I: FIBRINOPEPTIDE A-ALPHA


Theoretical massNumber of molelcules
Total (without water)110,61110
Polymers110,61110
Non-polymers00
Water13,205733
1
L: THROMBIN
H: THROMBIN
E: THROMBIN
F: FIBRINOPEPTIDE A-ALPHA


Theoretical massNumber of molelcules
Total (without water)36,8824
Polymers36,8824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint-52 kcal/mol
Surface area13120 Å2
MethodPISA
2
J: THROMBIN
K: THROMBIN
G: FIBRINOPEPTIDE A-ALPHA


Theoretical massNumber of molelcules
Total (without water)36,8643
Polymers36,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-17 kcal/mol
Surface area13070 Å2
MethodPISA
3
M: THROMBIN
N: THROMBIN
I: FIBRINOPEPTIDE A-ALPHA


Theoretical massNumber of molelcules
Total (without water)36,8643
Polymers36,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-14 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.470, 88.780, 98.550
Angle α, β, γ (deg.)90.00, 106.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein/peptide , 2 types, 6 molecules LJMFGI

#1: Protein/peptide THROMBIN


Mass: 5735.240 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III.
Source: (natural) Bos taurus (domestic cattle) / Tissue: BLOOD / References: UniProt: P00735, thrombin
#4: Protein/peptide FIBRINOPEPTIDE A-ALPHA


Mass: 1356.508 Da / Num. of mol.: 3 / Fragment: RESIDUES 7 - 19
Source method: isolated from a genetically manipulated source
Details: THREE COMPLEXES ARE PRESENTED, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN
References: UniProt: P12803, UniProt: P68108*PLUS

-
Protein , 3 types, 4 molecules HEKN

#2: Protein THROMBIN


Mass: 17525.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III.
Source: (natural) Bos taurus (domestic cattle) / Tissue: BLOOD / References: UniProt: P00735, thrombin
#3: Protein THROMBIN


Mass: 12265.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III.
Source: (natural) Bos taurus (domestic cattle) / Tissue: BLOOD / References: UniProt: P00735, thrombin
#5: Protein THROMBIN


Mass: 29772.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: BLOOD / References: UniProt: P00735, thrombin

-
Non-polymers , 1 types, 733 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsCHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / Details: Martin, P.D., (1992) J. Biol. Chem., 267, 7911.
Components of the solutions
*PLUS
Conc.: 40 % / Common name: ammonium sulfate

-
Data collection

DetectorType: SIEMENS / Detector: X1000 MULTIWIRE
ReflectionResolution: 2.2→7 Å / Num. obs: 45875 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.3 Å / Rsym value: 0.072 / % possible all: 15
Reflection
*PLUS
Num. measured all: 117995 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 15 %

-
Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORrefinement
XENGENdata scaling
RefinementResolution: 2.2→7 Å / Rfactor Rwork: 0.171 / Rfactor obs: 0.171 / σ(F): 1
Details: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA ...Details: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA THROMBIN. FIBRINOPEPTIDES I AND II HAVE OCCUPANCIES THAT MAKES THE AVERAGE SIDE CHAIN B OF OPR-16 ROUGHLY EQUAL TO THAT IN FIBRINOPEPTIDE III. THE DEPOSITORS DO NOT SEE ANY DENSITY AT ALL FOR THROMBIN RESIDUES 1U - 1I, AND POOR DENSITY FOR THE N AND C TERMINI OF THE LIGHT CHAINS, THE C TERMINUS OF THE HEAVY CHAINS, AND THE FIVE RESIDUES BORDERING 149B IN MOLECULES II AND III.
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7451 0 0 733 8184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

+
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