1NCO | pdb_00001nco

STRUCTURE OF THE ANTITUMOR PROTEIN-CHROMOPHORE COMPLEX NEOCARZINOSTATIN

• PDB DOI: https://doi.org/10.2210/pdb1NCO/pdb

• Classification: ANTIBACTERIAL AND ANTITUMOR PROTEIN
• Organism(s): Streptomyces carzinostaticus
• Mutation(s): No 


• Deposited: 1993-07-13 Released: 1993-10-31 
• Deposition Author(s): Kim, K.-H., Kwon, B.-M., Myers, A.G., Rees, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of neocarzinostatin, an antitumor protein-chromophore complex.

Kim, K.H., Kwon, B.M., Myers, A.G., Rees, D.C.

(1993) Science 262: 1042-1046

• PubMed: 8235619 
• DOI: https://doi.org/10.1126/science.8235619
• Primary Citation Related Structures: 
  1NCO


• PubMed Abstract: 
  

  Structures of the protein-chromophore complex and the apoprotein form of neocarzinostatin were determined at 1.8 angstrom resolution. Neocarzinostatin is composed of a labile chromophore with DNA-cleaving activity and a stabilizing protein. The chromophore displays marked nonlinearity of the triple bonds and is bound noncovalently in a pocket formed by the two protein domains. The chromophore pi-face interacts with the phenyl ring edges of Phe52 and Phe78. The amino sugar and carbonate groups of the chromophore are solvent exposed, whereas the epoxide, acetylene groups, and carbon C-12, the site of nucleophilic thiol addition during chromophore activation, are unexposed. The position of the amino group of the chromophore carbohydrate relative to C-12 supports the idea that the amino group plays a role in thiol activation.

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Organizational Affiliation: 
• Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.98 kDa 
• Atom Count: 1,773 
• Modeled Residue Count: 226 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HOLO-NEOCARZINOSTATIN	A, B	113	Streptomyces carzinostaticus	Mutation(s): 0
UniProt
Find proteins for P0A3R9 (Streptomyces carzinostaticus) Explore P0A3R9  Go to UniProtKB:  P0A3R9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CHR	D [auth B]	NEOCARZINOSTATIN-CHROMOPHORE C35 H33 N O12 QZGIWPZCWHMVQL-UIYAJPBUSA-N
MRD	C [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.4	α = 90
b = 90.4	β = 90
c = 52.5	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Kim, K.-H., Kwon, B.-M., Myers, A.G., Rees, D.C.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-09
  Changes: Structure summary