1QFI | pdb_00001qfi

SYNTHESIS AND STRUCTURE OF PROLINE RING MODIFIED ACTINOMYCINS OF X TYPE

• PDB DOI: https://doi.org/10.2210/pdb1QFI/pdb

• Classification: ANTIBIOTIC
• Organism(s): Streptomyces antibioticus
• Mutation(s): No 


• Deposited: 1999-04-12 Released: 2003-07-15 
• Deposition Author(s): Lifferth, A., Bahner, I., Lackner, H., Schaefer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.91 Å
• R-Value Work: 
  0.080 (DCC) 

Literature

Synthesis and Structure of Proline Ring Modified Actinomycins of the X-Type

Lifferth, A., Bahner, I., Lackner, H., Schaefer, M.

(1999) Z Naturforsch C Biosci 54: 681

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.69 kDa 
• Atom Count: 327 
• Modeled Residue Count: 33 
• Deposited Residue Count: 33 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTINOMYCIN X2	A, B, C	11	Streptomyces antibioticus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EEE	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth C], L [auth C]	ETHYL ACETATE C4 H8 O2 XEKOWRVHYACXOJ-UHFFFAOYSA-N
MOH	I [auth A], K [auth C], M [auth C], N [auth C], O [auth C]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPL	A, B, C	L-PEPTIDE LINKING	C5 H7 N O3		PRO
MVA	A, B, C	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	A, B, C	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000007	A, B, C	Actinomycin X2	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.91 Å
• R-Value Work:  0.080 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 15.594	α = 86.23
b = 16.009	β = 85.16
c = 25.322	γ = 69.65

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SAINT	data reduction
SADABS	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-15 
Deposition Author(s): Lifferth, A., Bahner, I., Lackner, H., Schaefer, M.

Revision History  

• Version 1.0: 2003-07-15
  Type: Initial release
  
• Version 1.1: 2011-06-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2012-12-12
  Changes: Other
• Version 1.5: 2017-10-04
  Changes: Advisory, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 3.0: 2024-07-10
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2024-10-09
  Changes: Structure summary