[English] 日本語
Yorodumi
- PDB-1xy1: CRYSTAL STRUCTURE ANALYSIS OF DEAMINO-OXYTOCIN. CONFORMATIONAL FL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xy1
TitleCRYSTAL STRUCTURE ANALYSIS OF DEAMINO-OXYTOCIN. CONFORMATIONAL FLEXIBILITY AND RECEPTOR BINDING
ComponentsBETA-MERCAPTOPROPIONATE-OXYTOCIN
KeywordsHORMONE
Function / homology
Function and homology information


Vasopressin-like receptors / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / neuropeptide hormone activity / G alpha (q) signalling events / secretory granule / response to estrogen / positive regulation of cold-induced thermogenesis / extracellular space
Similarity search - Function
Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones
Similarity search - Domain/homology
Oxytocin-neurophysin 1
Similarity search - Component
MethodX-RAY DIFFRACTION / Resolution: 1.04 Å
AuthorsHusain, J. / Blundell, T.L. / Wood, S.P. / Tickle, I.J. / Cooper, S. / Pitts, J.E.
Citation
Journal: Science / Year: 1986
Title: Crystal structure analysis of deamino-oxytocin: conformational flexibility and receptor binding.
Authors: Wood, S.P. / Tickle, I.J. / Treharne, A.M. / Pitts, J.E. / Mascarenhas, Y. / Li, J.Y. / Husain, J. / Cooper, S. / Blundell, T.L. / Hruby, V.J. / Buku, A. / Fischman, A.J. / Wyssbrod, H.R.
#1: Journal: Biological Organization. Macromolecular Interactions at High Resolution
Year: 1987
Title: X-Ray Analysis of Deamino-Oxytocin. Conformational Flexibility and Receptor Binding
Authors: Pitts, J.E. / Wood, S.P. / Tickle, I.J. / Treharne, A.M. / Mascarenhas, Y. / Li, J.Y. / Husain, J. / Cooper, S. / Blundell, T.L. / Hruby, V.J. / Wyssbrod, H.R. / Baku, A. / Fischman, A.J.
#2: Journal: Crystallography in Molecular Biology / Year: 1988
Title: X-Ray Analysis of Polypeptide Hormones at (Less Than or Equal) 1 Angstrom Resolution. Anisotropic Thermal Motion and Secondary Structure of Pancreatic Polypeptide and Deamino-Oxytocin
Authors: Treharne, A.M. / Wood, S.P. / Tickle, I.J. / Pitts, J.E. / Husain, J. / Glover, I.D. / Cooper, S. / Blundell, T.L.
History
DepositionJun 5, 1987Processing site: BNL
Revision 1.0Apr 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Revision 1.5Nov 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-MERCAPTOPROPIONATE-OXYTOCIN
B: BETA-MERCAPTOPROPIONATE-OXYTOCIN


Theoretical massNumber of molelcules
Total (without water)1,9862
Polymers1,9862
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.270, 9.040, 23.040
Angle α, β, γ (deg.)90.00, 102.24, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: THE SG ATOM OF RESIDUE MPR A 1 AND MPR B 1 IS DISORDERED. THE TWO POSSIBLE SITES FOR THIS ATOM ARE GIVEN AS ALTERNATE LOCATIONS *A* AND *B*.
2: THERMAL PARAMETERS FOR SOME HYDROGEN ATOMS WERE DEPOSITED WITH VALUES LESS THAN 0.05. CONVERSION TO UEQ GENERATES A THERMAL PARAMETER OF 0.00 BECAUSE OF PROTEIN DATA BANK FORMAT SPECIFICATION FOR THIS FIELD.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9977, -0.0662, 0.0109), (-0.0652, 0.9951, 0.0745), (-0.0158, 0.0745, -0.9972)
Vector: 0.033, 0.02, -0.006)

-
Components

#1: Protein/peptide BETA-MERCAPTOPROPIONATE-OXYTOCIN


Mass: 993.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: UniProt: P01175*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: Chiu, C.C., (1969) Science, 163, 925.

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameClassification
SHELXmodel building
SHELX-76refinement
SHELXphasing
RefinementHighest resolution: 1.04 Å
Refinement stepCycle: LAST / Highest resolution: 1.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms136 0 0 13 149
Refinement
*PLUS
Num. reflection obs: 4681 / Rfactor obs: 0.088
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