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(-) Description

Title :  NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT
 
Authors :  M. Gochin
Date :  08 Mar 00  (Deposition) - 20 Mar 00  (Release) - 28 Dec 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (6x)
NMR Structure *:  A,B  (1x)
Keywords :  Drug Bound In The Minor Groove Of Dna, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Gochin
A High-Resolution Structure Of A Dna-Chromomycin-Co(Ii) Complex Determined From Pseudocontact Shifts In Nuclear Magnetic Resonance.
Structure Fold. Des. V. 8 441 2000
PubMed-ID: 10801486  |  Reference-DOI: 10.1016/S0969-2126(00)00124-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3')
    Chains: A, B
    Engineered: YES
    Other Details: TWO MOLECULES OF THE DRUG CHROMOMYCIN A3 (1GL-2GL-DXB- DDA-DDA-1AR, CHAINS C, AND D) ARE BOUND IN THE MINOR GROOVE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
NMR Structure (6x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

NMR Structure (6, 13)
No.NameCountTypeFull Name
11GL2Ligand/Ion4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
22GL2Ligand/Ion4-O-ACETYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
3CO1Ligand/IonCOBALT (II) ION
4CPH2Ligand/Ion1,8-DIHYDROXY-7-METHYL-3-(1,3,4-TRIHYDROXY-2-OXO-PENTYL)-3,10-DIHYDRO-2H-ANTHRACEN-9-ONE
5DDA4Ligand/Ion2,6-DIDEOXY-BETA-D-GLUCOSE
6ERI2Ligand/Ion4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE
NMR Structure * (5, 12)
No.NameCountTypeFull Name
11GL2Ligand/Ion4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
22GL2Ligand/Ion4-O-ACETYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
3CO-1Ligand/IonCOBALT (II) ION
4CPH2Ligand/Ion1,8-DIHYDROXY-7-METHYL-3-(1,3,4-TRIHYDROXY-2-OXO-PENTYL)-3,10-DIHYDRO-2H-ANTHRACEN-9-ONE
5DDA4Ligand/Ion2,6-DIDEOXY-BETA-D-GLUCOSE
6ERI2Ligand/Ion4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE

(-) Sites  (13, 13)

NMR Structure (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDG B:14 , DC B:15 , 2GL B:22 , ERI B:34BINDING SITE FOR RESIDUE 1GL B 21
02AC2SOFTWAREDG B:14 , DC B:15 , 1GL B:21 , CPH B:23 , ERI B:34 , DDA B:35BINDING SITE FOR RESIDUE 2GL B 22
03AC3SOFTWAREDG A:3 , 2GL A:32 , CPH A:33 , DA B:17 , DA B:18 , DDA B:25BINDING SITE FOR RESIDUE ERI B 24
04AC4SOFTWARE2GL A:32 , CPH A:33 , ERI B:24 , DDA B:26BINDING SITE FOR RESIDUE DDA B 25
05AC5SOFTWARECPH A:33 , DC B:16 , CPH B:23 , DDA B:25BINDING SITE FOR RESIDUE DDA B 26
06AC6SOFTWAREDG A:4 , DC A:5 , 2GL A:32BINDING SITE FOR RESIDUE 1GL A 31
07AC7SOFTWAREDG A:4 , DC A:5 , 1GL A:31 , CPH A:33 , ERI B:24 , DDA B:25BINDING SITE FOR RESIDUE 2GL A 32
08AC8SOFTWAREDA A:7 , DG B:13 , DG B:14 , 1GL B:21 , 2GL B:22 , CPH B:23 , DDA B:35BINDING SITE FOR RESIDUE ERI B 34
09AC9SOFTWARE2GL B:22 , CPH B:23 , ERI B:34 , DDA B:36BINDING SITE FOR RESIDUE DDA B 35
10BC1SOFTWARECPH A:33 , DDA B:35BINDING SITE FOR RESIDUE DDA B 36
11BC2SOFTWARECPH A:33 , CPH B:23BINDING SITE FOR RESIDUE CO A 41
12BC3SOFTWAREDC A:6 , CPH A:33 , CO A:41 , DG B:13 , DG B:14 , DC B:15 , DC B:16 , 2GL B:22 , DDA B:26 , ERI B:34 , DDA B:35BINDING SITE FOR RESIDUE CPH B 23
13BC4SOFTWAREDG A:3 , DG A:4 , DC A:5 , DC A:6 , DA A:7 , 2GL A:32 , CO A:41 , DC B:16 , CPH B:23 , ERI B:24 , DDA B:25 , DDA B:26 , DDA B:36BINDING SITE FOR RESIDUE CPH A 33

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EKH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EKH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EKH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EKH)

(-) Exons   (0, 0)

(no "Exon" information available for 1EKH)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:8
                                       
                  1ekh A  1 TTGGCCAA  8


Chain B from PDB  Type:DNA  Length:8
                                       
                  1ekh B 11 TTGGCCAA 18
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

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(no "SCOP Domain" information available for 1EKH)

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(no "CATH Domain" information available for 1EKH)

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(no "Pfam Domain" information available for 1EKH)

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 1EKH)

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1eki THE AVERAGE STRUCTURE