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- PDB-1xy1: CRYSTAL STRUCTURE ANALYSIS OF DEAMINO-OXYTOCIN. CONFORMATIONAL FL... -

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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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

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

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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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

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