3CDM - JenaLib

Title :   STRUCTURAL ADAPTATION AND CONSERVATION IN QUADRUPLEX-DRUG RECOGNITION

Authors :   G. N. Parkinson, S. Neidle

Date :   27 Feb 08 (Deposition) - 23 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Quadruplex, Dna, Propeller, Intramolecular, Human Telomere Parallel Stranded, Ligand, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. N. Parkinson, F. Cuenca, S. Neidle
Topology Conservation And Loop Flexibility In Quadruplex-Drug Recognition: Crystal Structures Of Inter- And Intramolecular Telomeric Dna Quadruplex-Drug Complexes
J. Mol. Biol. V. 381 1145 2008
PubMed-ID: 18619463 | Reference-DOI: 10.1016/J.JMB.2008.06.022
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	K	4	Ligand/Ion	POTASSIUM ION
2	NII	6	Ligand/Ion	2,7-BIS[3-(DIMETHYLAMINO)PROPYL]-4,9-BIS[(3-HYDROXYPROPYL)AMINO]BENZO[LMN][3,8]PHENANTHROLINE-1,3,6,8(2H,7H)-TETRONE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	NII	2	Ligand/Ion	2,7-BIS[3-(DIMETHYLAMINO)PROPYL]-4,9-BIS[(3-HYDROXYPROPYL)AMINO]BENZO[LMN][3,8]PHENANTHROLINE-1,3,6,8(2H,7H)-TETRONE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	NII	4	Ligand/Ion	2,7-BIS[3-(DIMETHYLAMINO)PROPYL]-4,9-BIS[(3-HYDROXYPROPYL)AMINO]BENZO[LMN][3,8]PHENANTHROLINE-1,3,6,8(2H,7H)-TETRONE

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	DG A:4 , DG A:5 , DG A:10 , DG A:11 , DG A:16 , DG A:17 , DG A:22 , DG A:23 , K A:25	BINDING SITE FOR RESIDUE K A 24
02	AC2	SOFTWARE	DG A:3 , DG A:4 , DG A:9 , DG A:10 , DG A:15 , DG A:16 , DG A:21 , DG A:22 , K A:24	BINDING SITE FOR RESIDUE K A 25
03	AC3	SOFTWARE	DG B:4 , DG B:5 , DG B:10 , DG B:11 , DG B:16 , DG B:17 , DG B:22 , DG B:23 , K B:25	BINDING SITE FOR RESIDUE K B 24
04	AC4	SOFTWARE	DG B:3 , DG B:4 , DG B:9 , DG B:10 , DG B:15 , DG B:16 , DG B:21 , DG B:22 , K B:24	BINDING SITE FOR RESIDUE K B 25
05	AC5	SOFTWARE	DG A:5 , DG A:11 , DG A:17 , DG A:23 , HOH A:36 , HOH A:53 , HOH A:56 , HOH A:65	BINDING SITE FOR RESIDUE NII A 26
06	AC6	SOFTWARE	DG A:3 , DG A:4 , DG A:9 , DG A:15 , DG A:21 , HOH A:39 , HOH A:43 , HOH A:45 , HOH A:55 , HOH A:57 , DG B:15 , DG B:21 , NII B:27	BINDING SITE FOR RESIDUE NII A 27
07	AC7	SOFTWARE	DG B:5 , DG B:11 , DG B:17 , DG B:23 , HOH B:73	BINDING SITE FOR RESIDUE NII B 26
08	AC8	SOFTWARE	NII A:27 , DG B:3 , DG B:9 , DG B:15 , DG B:21 , HOH B:60	BINDING SITE FOR RESIDUE NII B 27
09	AC9	SOFTWARE	DT A:7 , DA A:8 , DT A:19 , DT B:19 , DA B:20	BINDING SITE FOR RESIDUE NII B 28
10	BC1	SOFTWARE	DA A:8 , DT B:1 , DT B:7 , DA B:8 , DT B:18 , DT B:19 , HOH B:47 , HOH B:71	BINDING SITE FOR RESIDUE NII B 29

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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Chain A from PDB  Type:DNA  Length:22
                                                     
                  3cdm A  2 AGGGTTAGGGTTAGGGTTAGGG 23
                                    11        21

Chain B from PDB  Type:DNA  Length:23
                                                      
                  3cdm B  1 TAGGGTTAGGGTTAGGGTTAGGG 23
                                    10        20

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Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (0, 0)

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