2MB3

Solution structure of an intramolecular (3+1) human telomeric G-quadruplex bound to a telomestatin derivative

> Summary

Summary for 2MB3

Descriptor5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'
Functional Keywordsintramolecular g-quadruplex, human telomere, anticancer targets, macrocyclic hexaoxazole, telomestatin derivative, dna-dna inhibitor complex, dna/dna inhibitor
Total number of polymer chains1
Total molecular weight8278.63
Authors
Chung, W.J.,Heddi, B.,Tera, M.,Iida, K.,Nagasawa, K.,Phan, A.T. (deposition date: 2013-07-24, release date: 2013-08-28, modification date: 2013-09-25)
Primary citation
Chung, W.J.,Heddi, B.,Tera, M.,Iida, K.,Nagasawa, K.,Phan, A.T.
Solution structure of an intramolecular (3 + 1) human telomeric g-quadruplex bound to a telomestatin derivative.
J.Am.Chem.Soc., 135:13495-13501, 2013
PubMed: 23909929
DOI: 10.1021/ja405843r
MImport into Mendeley
Experimental method
SOLUTION NMR
NMR Information
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Structure validation

Clashscore9MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all NMR structures

More Asymmetric unit images

Molmil generated image of 2mb3
no rotation
Molmil generated image of 2mb3
rotated about x axis by 90°
Molmil generated image of 2mb3
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ADNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')polymer247591.91
(12S,27S)-12,27-BIS(4-AMINOBUTYL)-4,30-DIMETHYL-3,7,14,18,22,29-HEXAOXA-11,26,31,32,33,34,35,36-OCTAAZAHEPTACYCLO[26.2.1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]HEXATRIACONTA-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-DODECAENE-10,25-DIONEnon-polymer686.71

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight7591.9
Non-Polymers*Number of molecules1
Total molecular weight686.7
All*Total molecular weight8278.6
*Water molecules are not included.

> Experimental details

Spectrometer

Experimental method:SOLUTION NMR

Spectrometer IDSpectrometer makerSpectrometer modelSpectrometer typeSpectrometer field strength
1BrukerAMXBruker AMX600
2BrukerAMXBruker AMX700
3BrukerAMXBruker AMX400

Experiment

experiment idconditions idsolution idExperiment type
1322D 1H-1H TOCSY
2312D 1H-1H TOCSY
3312D 1H-1H NOESY
4322D 1H-1H NOESY
5122D 1H-1H NOESY
6222D 1H-1H NOESY
7322D 1H-13C HSQC aromatic
8252D 1H-13C HSQC aromatic
9322D 1H-13C HSQC aliphatic
10252D 1H-13C HSQC aliphatic
11242D 1H-13C HSQC aliphatic
12242D 1H-13C HSQC aromatic
13231D JRHMBC
14322D 1H-31P HSQC

NMR Sample

conditions idNMR sample pHNMR sample pressureNMR sample temperature
17ambient310
27298
37298

Conformers

Conformers Calculated Total Number100
Conformers Submitted Total Number10

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC19BINDING SITE FOR RESIDUE L2H A 25
ChainResidue
ADT2
ADG3
ADA8
ADG9
ADG17
ADT18
ADT19
ADA20
ADG21

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
L2H_2mb3_A_2512(12S,27S)-12,27-BIS(4-AMINOBUTYL)-4,30-DIMETHYL-3,7,14,18,22,29-HEXAOXA-11,26,31,32,33,34,35,36-OCTAAZAHEPTACYCLO[26.2.1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]HEXATRIACONTA-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-DODECAENE-10,25-DIONE binding site
ChainResidueligand
ADT1-DG3L2H: (12S,27S)-12,27-BIS(4-AMINOBUTYL)-4,30-DIMETHYL-3,7,14,18,22,29-HEXAOXA-11,26,31,32,33,34,35,36-OCTAAZAHEPTACYCLO[26.2.1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]HEXATRIACONTA-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-DODECAENE-10,25-DIONE
ADT7-DG9L2H: (12S,27S)-12,27-BIS(4-AMINOBUTYL)-4,30-DIMETHYL-3,7,14,18,22,29-HEXAOXA-11,26,31,32,33,34,35,36-OCTAAZAHEPTACYCLO[26.2.1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]HEXATRIACONTA-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-DODECAENE-10,25-DIONE
ADG17-DG21L2H: (12S,27S)-12,27-BIS(4-AMINOBUTYL)-4,30-DIMETHYL-3,7,14,18,22,29-HEXAOXA-11,26,31,32,33,34,35,36-OCTAAZAHEPTACYCLO[26.2.1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]HEXATRIACONTA-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-DODECAENE-10,25-DIONE
ADG10L2H: (12S,27S)-12,27-BIS(4-AMINOBUTYL)-4,30-DIMETHYL-3,7,14,18,22,29-HEXAOXA-11,26,31,32,33,34,35,36-OCTAAZAHEPTACYCLO[26.2.1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]HEXATRIACONTA-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-DODECAENE-10,25-DIONE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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