[English] 日本語
Yorodumi
- PDB-2pik: CALICHEAMICIN GAMMA1I-DNA COMPLEX, NMR, 6 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pik
TitleCALICHEAMICIN GAMMA1I-DNA COMPLEX, NMR, 6 STRUCTURES
ComponentsDNA(5'-D(C*AP*CP*TP*CP*CP*TP*GP*GP*TP*TP*TP*TP* TP*GP*TP*GP*AP*GP*GP*AP*CP*CP)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / CALICHEAMICIN GAMMA1I - DNA COMPLEX / ENEDIYNE ALIGNMENT IN MINOR GROOVE / SACCHARIDE DNA MINOR GROOVE INTERACTIONS / INTERMOLECULAR DRUG IODINE-GUANINE AMINO PROTON INTERACTIONS / SPECIFICITY AND CLEAVAGE PROCESS
Function / homology2,6-dideoxy-4-thio-beta-D-allopyranose / Chem-HIB / 3-O-methyl-alpha-L-rhamnopyranose / Chem-MTC / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsKumar, R.A. / Ikemoto, N. / Patel, D.J.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Solution structure of the calicheamicin gamma 1I-DNA complex.
Authors: Kumar, R.A. / Ikemoto, N. / Patel, D.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Calicheamicin-DNA Complexes: Warhead Alignment and Saccharide Recognition of the Minor Groove
Authors: Ikemoto, N. / Kumar, R.A. / Ling, T.T. / Ellestad, G.A. / Danishefsky, S.J. / Patel, D.J.
History
DepositionDec 31, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_oper_list / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.1May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA(5'-D(C*AP*CP*TP*CP*CP*TP*GP*GP*TP*TP*TP*TP* TP*GP*TP*GP*AP*GP*GP*AP*CP*CP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4476
Polymers7,0391
Non-polymers1,4085
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 6
Representative

-
Components

-
DNA chain , 1 types, 1 molecules A

#1: DNA chain DNA(5'-D(C*AP*CP*TP*CP*CP*TP*GP*GP*TP*TP*TP*TP* TP*GP*TP*GP*AP*GP*GP*AP*CP*CP)-3')


Mass: 7038.531 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Sugars , 3 types, 3 molecules

#2: Polysaccharide 2,4-dideoxy-4-(ethylamino)-3-O-methyl-alpha-L-threo-pentopyranose-(1-2)-4-amino-4,6-dideoxy-beta-D- ...2,4-dideoxy-4-(ethylamino)-3-O-methyl-alpha-L-threo-pentopyranose-(1-2)-4-amino-4,6-dideoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 320.382 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122m-1b_1-5_4*N][ad21h-1a_1-5_3*OC_4*NCC]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-6-deoxy-Glcp4N]{[(2+1)][a-L-2-deoxy-Xylp3Me4N]{[(4+1)][ethyl]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-DSR / 2,6-dideoxy-4-thio-beta-D-allopyranose / 2,6-dideoxy-4-thio-beta-D-allose / 2,6-dideoxy-4-thio-D-allose / 2,6-dideoxy-4-thio-allose


Type: D-saccharide, beta linking / Mass: 164.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O3S
IdentifierTypeProgram
b-D-2,6-deoxy-Allp4SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Sugar ChemComp-MRP / 3-O-methyl-alpha-L-rhamnopyranose / 3-O-METHYL-ALPHA-L-RHAMNOPYRANOSIDE / 6-deoxy-3-O-methyl-alpha-L-mannopyranose / 3-O-methyl-alpha-L-rhamnose / 3-O-methyl-L-rhamnose / 3-O-methyl-rhamnose


Type: L-saccharide, alpha linking / Mass: 178.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O5
IdentifierTypeProgram
a-L-Rhap3OMeIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 2 types, 2 molecules

#4: Chemical ChemComp-HIB / 4-HYDROXY-5-IODO-2,3-DIMETHOXY-6-METHYLBENZOIC ACID


Mass: 338.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11IO5
#6: Chemical ChemComp-MTC / [1,8-DIHYDROXY-11-OXO-13-(2-METHYLTRITHIO-ETHYLIDENE)-BICYCLO[7.3.1]TRIDECA-4,9-DIENE-2,6-DIYN-10-YL]-CARBAMIC ACID METHYL ESTER


Mass: 407.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17NO4S3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditions
Conditions-IDpHTemperature (K)
17283 K
27278 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformers calculated total number: 6 / Conformers submitted total number: 6

+
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