[English] 日本語
Yorodumi
- PDB-1hdq: Crystal structure of bovine pancreatic carboxypeptidase A complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hdq
TitleCrystal structure of bovine pancreatic carboxypeptidase A complexed with D-N-hydroxyaminocarbonyl phenylalanine at 2.3 A
ComponentsCARBOXYPEPTIDASE A
KeywordsCARBOXYPEPTIDASE / CPA / LBHB / INHIBITOR
Function / homology
Function and homology information


carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A ...Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE / Carboxypeptidase A1
Similarity search - Component
Biological speciesBOS BOVIS (domestic cattle)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsCho, J.H. / Ha, N.-C. / Chung, S.J. / Kim, D.H. / Choi, K.Y. / Oh, B.-H.
CitationJournal: Bioorg.Med.Chem. / Year: 2002
Title: Insight Into the Stereochemistry in the Inhibition of Carboxypeptidase a with N-(Hydroxyaminocarbonyl)Phenylalanine: Binding Modes of an Enantiomeric Pair of the Inhibitor to Carboxypeptidase A
Authors: Cho, J.H. / Kim, D.H. / Chung, S.J. / Ha, N.-C. / Oh, B.-H. / Choi, K.Y.
History
DepositionNov 17, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8073
Polymers34,5171
Non-polymers2902
Water3,801211
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.961, 60.465, 47.792
Angle α, β, γ (deg.)90.00, 97.59, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL_UNIT: MONOMER

-
Components

#1: Protein CARBOXYPEPTIDASE A


Mass: 34517.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS BOVIS (domestic cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Chemical ChemComp-INF / D-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE


Mass: 224.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPEPTIDYL-L-AMINO ACID + H(2)O = PEPTIDE + L-AMINO ACID THE ZYMOGEN IS SECRETED AS A TERNARY COMPLEX ...PEPTIDYL-L-AMINO ACID + H(2)O = PEPTIDE + L-AMINO ACID THE ZYMOGEN IS SECRETED AS A TERNARY COMPLEX COMPOSED OF PROCARBOXYPEPTIDASE A, CHYMOTRYPSINOGEN C AND PROPROTEINASE E. ALSO KNOWN AS THE ZINC CARBOXYPEPTIDASE FAMILY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein11
20.02 MTris-HCl11pH7.5
31.2 M11LiCl
40.14 M12pH7.5LiCl

-
Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 13199 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 33
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % possible obs: 96 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 82.2 % / Rmerge(I) obs: 0.094

-
Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.3→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 -5 %RANDOM
Rwork0.1388 ---
obs0.1388 12659 96 %-
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 17 211 2670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.172

+
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