NMR Ensemble

1BP8

4:2:1 mithramycin:Mg++:d(ACCCGGGT)2 complex

Structural Biology Knowledgebase: 1BP8 SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 7
  • Conformers Submitted: 1
  • Selection Criteria:

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1BP8

Classification: DNA

Total Structure Weight: 9332.67

Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*CP*CP*CP*GP*GP*GP*T)-3' A, B 8 synthetic 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++

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DXB
Query on DXB

A, B 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2- OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYDROXY-7- METHYL-ANTHRACENE
C21 H24 O7
XBKVKSRQTHGEJA-LAHPPJGFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MDA
Query on MDA

A, B 2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE
C7 H14 O4
YQLFLCVNXSPEKQ-GBNDHIKLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DDA
Query on DDA

A, B 2,6-DIDEOXY-BETA-D-GLUCOSE
2,6-DIDEOXY-BETA-D-MANNOSE (Synonym)
C6 H12 O4
FDWRIIDFYSUTDP-KVTDHHQDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DDL
Query on DDL

A, B 2,6-DIDEOXY-BETA-D-GALACTOSE
2,6-DIDEOXY-BETA-D-TALOSE (Synonym)
C6 H12 O4
FDWRIIDFYSUTDP-KAZBKCHUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 7
  • Conformers Submitted: 1
  • Selection Criteria: --

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1998-08-13
  • Released Date: 1999-08-16
  • Deposition author(s): Keniry, M.A., Owen, E.A., Shafer, R.H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4