[English] 日本語
Yorodumi
- PDB-1bp8: 4:2:1 mithramycin:Mg++:d(ACCCGGGT)2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bp8
Title4:2:1 mithramycin:Mg++:d(ACCCGGGT)2 complex
Components5'-D(*AP*CP*CP*CP*GP*GP*GP*T)-3'
KeywordsDNA / MITHRAMYCIN / OLIGONUCLEOTIDE
Function / homologyChem-DXB / DNA
Function and homology information
MethodSOLUTION NMR / FULL RELAXATION MATRIX ANALYSIS, RESTRAINED MOLECULAR DYNAMICS
AuthorsKeniry, M.A. / Owen, E.A. / Shafer, R.H.
CitationJournal: Biopolymers / Year: 2000
Title: The three-dimensional structure of the 4:1 mithramycin:d(ACCCGGGT)2 complex: evidence for an interaction between the E saccharides
Authors: Keniry, M.A. / Owen, E.A. / Shafer, R.H.
History
DepositionAug 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / ndb_struct_conf_na ...atom_site / ndb_struct_conf_na / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*AP*CP*CP*CP*GP*GP*GP*T)-3'
B: 5'-D(*AP*CP*CP*CP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,26116
Polymers4,8552
Non-polymers4,40514
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9960 Å2
ΔGint125 kcal/mol
Surface area1860 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 7
Representative

-
Components

#1: DNA chain 5'-D(*AP*CP*CP*CP*GP*GP*GP*T)-3'


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: FOUR MOLECULES OF MITHRAMYCIN (PLICAMYCIN) (RESIDUES DDA-DDA-DXB-DDA-DDL-DDB, CHAINS C, D, E, F) BOUND IN THE MINOR GROOVE. Oxygens of the MITHRAMYCIN chromophore (residue DXB) are complexed with Mg++
#2: Polysaccharide
beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose


Type: oligosaccharide / Mass: 278.299 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DOlib1-3DOlib1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[ad122m-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2,6-deoxy-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide
2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta- ...2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta-D-Olivopyranose


Type: oligosaccharide / Mass: 422.468 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,3,2/[ad122m-1b_1-5][ad112m-1b_1-5][ad622m-1b_1-5_3*C]/1-2-3/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2-deoxy-Fucp]{[(3+1)][b-D-2,6-deoxy-Allp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-DXB / 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYDROXY-7-METHYL-ANTHRACENE


Mass: 388.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24O7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121PCOSY
131TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR TWO DIMENSIONAL NMR SPECTROSCOPY

-
Sample preparation

Sample conditionspH: 7.2 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA 600 / Manufacturer: Varian / Model: INOVA 600 / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CHARMM23.2MSI, WALTHAM , MArefinement
VNMRstructure solution
MARDIGRASstructure solution
CORMA CHARMMCHARMMstructure solution
RefinementMethod: FULL RELAXATION MATRIX ANALYSIS, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE
NMR ensembleConformers calculated total number: 7 / Conformers submitted total number: 1

+
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