1QMS

Head-to-Tail Dimer of Calicheamicin gamma-1-I Oligosaccharide Bound to DNA Duplex, NMR, 9 Structures

• PDB DOI: https://doi.org/10.2210/pdb1QMS/pdb
• NAKB: 1QMS

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 1999-10-06 Released: 1999-10-12 
• Deposition Author(s): Bifulco, G., Galeone, A., Nicolaou, K.C., Chazin, W.J., Gomez-Paloma, L.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 9 
• Selection Criteria: LOWEST RESTRAINT VIOLATION 

Literature

Solution Structure of the Complex between the Head-to-Tail Dimer of Calicheamicin Gamma-1-I Oligosaccharide and a DNA Duplex Containing D(ACCT) and D(TCCT) High-Affinity Binding Sites

Bifulco, G., Galeone, A., Nicolaou, K.C., Chazin, W.J., Gomez-Paloma, L.

(1998) J Am Chem Soc 120: 7183-7191

• DOI: https://doi.org/10.1021/ja973910y

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 9.34 kDa 
• Atom Count: 608 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*CP*CP*TP*TP*CP*CP*TP*GP*C)-3')	A	12	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*GP*GP*AP*AP*GP*GP*TP*GP*C)-3')	B	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CCI	C [auth B], E [auth B]	CALICHEAMICIN GAMMA-1-OLIGOSACCHARIDE C38 H61 I N2 O17 S LLRIDSCDUGRTJE-MKLYLBDDSA-N
NBU	D [auth B]	N-BUTANE C4 H10 IJDNQMDRQITEOD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CCI	PDBBind:	Kd: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 9 
• Selection Criteria: LOWEST RESTRAINT VIOLATION 

Structure Validation

Currently 1QMS does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 1999-10-12 
Deposition Author(s): Bifulco, G., Galeone, A., Nicolaou, K.C., Chazin, W.J., Gomez-Paloma, L.

Revision History  

• Version 1.0: 1999-10-12
  Type: Initial release
  
• Version 1.1: 2012-02-08
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2013-03-27
  Changes: Derived calculations, Non-polymer description
• Version 1.3: 2018-03-07
  Changes: Database references, Source and taxonomy
• Version 1.4: 2019-05-08
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-05-15
  Changes: Data collection, Database references, Derived calculations, Other