[English] 日本語
Yorodumi
- PDB-2pka: REFINED 2 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF PORCINE PANCREATIC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pka
TitleREFINED 2 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF PORCINE PANCREATIC KALLIKREIN A, A SPECIFIC TRYPSIN-LIKE SERINE PROTEINASE. CRYSTALLIZATION, STRUCTURE DETERMINATION, CRYSTALLOGRAPHIC REFINEMENT, STRUCTURE AND ITS COMPARISON WITH BOVINE TRYPSIN
Components(KALLIKREIN A) x 2
KeywordsSERINE PROTEINASE
Function / homology
Function and homology information


tissue kallikrein / regulation of systemic arterial blood pressure / zymogen activation / secretory granule / serine-type endopeptidase activity / extracellular space
Similarity search - Function
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 ...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
BENZAMIDINE / Glandular kallikrein
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsBode, W. / Chen, Z.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Refined 2 A X-ray crystal structure of porcine pancreatic kallikrein A, a specific trypsin-like serine proteinase. Crystallization, structure determination, crystallographic refinement, ...Title: Refined 2 A X-ray crystal structure of porcine pancreatic kallikrein A, a specific trypsin-like serine proteinase. Crystallization, structure determination, crystallographic refinement, structure and its comparison with bovine trypsin.
Authors: Bode, W. / Chen, Z. / Bartels, K. / Kutzbach, C. / Schmidt-Kastner, G. / Bartunik, H.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Refined 2.5 Angstroms X-Ray Crystal Structure of the Complex Formed by Porcine Kallikrein a and the Bovine Pancreatic Trypsin Inhibitor. Crystallization, Patterson Search, Structure ...Title: Refined 2.5 Angstroms X-Ray Crystal Structure of the Complex Formed by Porcine Kallikrein a and the Bovine Pancreatic Trypsin Inhibitor. Crystallization, Patterson Search, Structure Determination, Refinement, Structure and Comparison with its Components and with the Bovine Trypsin-Pancreatic Trypsin Inhibitor Complex
Authors: Chen, Z. / Bode, W.
History
DepositionMay 21, 1984Processing site: BNL
Revision 1.0Jul 19, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KALLIKREIN A
B: KALLIKREIN A
X: KALLIKREIN A
Y: KALLIKREIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5026
Polymers51,2614
Non-polymers2402
Water1,53185
1
A: KALLIKREIN A
B: KALLIKREIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7513
Polymers25,6312
Non-polymers1201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-41 kcal/mol
Surface area10580 Å2
MethodPISA
2
X: KALLIKREIN A
Y: KALLIKREIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7513
Polymers25,6312
Non-polymers1201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-44 kcal/mol
Surface area10320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-93 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.200, 90.200, 159.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: RESIDUES PRO B 147, PRO B 219, PRO Y 147, PRO Y 219 ARE CIS-PROLINES.
2: SEE REMARK 5.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3872, -0.83477, 0.39152), (0.68544, 0.54462, 0.48328), (-0.61662, 0.08124, 0.78303)
Vector: 36.314, -49.058, 24.735)
DetailsTHE TRANSFORMATION GIVING OPTIMAL SUPERPOSITION OF MOLECULE 1 (CHAIN INDICATORS *A* AND *B*) ONTO MOLECULE 2 (CHAIN INDICATORS *X* AND *Y*) IS GIVEN IN THE MTRIX RECORDS BELOW.

-
Components

#1: Protein KALLIKREIN A


Mass: 9119.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00752, tissue kallikrein
#2: Protein KALLIKREIN A


Mass: 16511.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00752, tissue kallikrein
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 Mammonium sulfate1drop
20.1 Mphosphate1drop
310 mMbenzamidine1drop
460 mg/mlprotein1drop

-
Data collection

Reflection
*PLUS
Highest resolution: 2.05 Å / Num. obs: 35517 / % possible obs: 86.8 % / Observed criterion σ(I): 2 / Num. measured all: 198249 / Rmerge(I) obs: 0.102

-
Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.22 / Highest resolution: 2.05 Å
Details: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP AND THAT THE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA.
Refinement stepCycle: LAST / Highest resolution: 2.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 18 85 3701
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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