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.

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
EEE Query on EEE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth C] SDF format, chain J [auth C] SDF format, chain H [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth C] MOL2 format, chain H [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth C] mmCIF format, chain H [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth C]
MOH Query on MOH Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth C] SDF format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A]	I [auth A], K [auth C], M [auth C], N [auth C], O [auth C]	METHANOL C H₄ O OKKJLVBELUTLKV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPL Query on DPL	A, B, C	L-PEPTIDE LINKING	C₅ H₇ N O₃		PRO
DVA Query on DVA	A, B, C	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--
MVA Query on MVA	A, B, C	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on 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 Query on PRD_000007	A, B, C	Actinomycin X2	Polypeptide / Antibiotic		Interactions Focus chain A Focus chain B Focus chain C Interactions & Density Focus chain A Focus chain B Focus chain C

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

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Entry History

Deposition Data

Released Date: 2003-07-15

Deposition Author(s):

Revision History (Full details and data files)

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