4HP7 | pdb_00004hp7

Trioxacarcin D517 as a product of guanine robbery from d(AACCGGTT)

PDB DOI: https://doi.org/10.2210/pdb4HP7/pdb

Classification: ANTIBIOTIC

Deposited: 2012-10-23 Released: 2013-10-23
Deposition Author(s): Smaltz, D.J., Magauer, T., Proepper, K., Dittrich, B., Myers, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free:
0.216 (Depositor), 0.180 (DCC)
R-Value Work:
0.180 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Trioxacarcin D517

Smaltz, D.J., Magauer, T., Proepper, K., Dittrich, B., Myers, A.G.

To be published.

Macromolecule Content

Total Structure Weight: 3.48 kDa
Atom Count: 259

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
18Y Query on 18Y Download Ideal Coordinates CCD File SDF format, chain A SDF format, chain E [auth C] SDF format, chain G [auth D] SDF format, chain C [auth B] MOL2 format, chain A MOL2 format, chain E [auth C] MOL2 format, chain G [auth D] MOL2 format, chain C [auth B] mmCIF format, chain A mmCIF format, chain E [auth C] mmCIF format, chain G [auth D] mmCIF format, chain C [auth B]	A, C [auth B], E [auth C], G [auth D]	Trioxacarcin A analogue, bound form C₃₃ H₄₀ O₁₄ VSONDVKNAFWAKH-UEXNXLFMSA-N		Interactions Focus chain A Focus chain C [auth B] Focus chain E [auth C] Focus chain G [auth D] Interactions & Density Focus chain A Focus chain C [auth B] Focus chain E [auth C] Focus chain G [auth D]
GUN Query on GUN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth B] SDF format, chain F [auth C] SDF format, chain H [auth D] MOL2 format, chain B [auth A] MOL2 format, chain D [auth B] MOL2 format, chain F [auth C] MOL2 format, chain H [auth D] mmCIF format, chain B [auth A] mmCIF format, chain D [auth B] mmCIF format, chain F [auth C] mmCIF format, chain H [auth D]	B [auth A], D [auth B], F [auth C], H [auth D]	GUANINE C₅ H₅ N₅ O UYTPUPDQBNUYGX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth B] Focus chain F [auth C] Focus chain H [auth D] Interactions & Density Focus chain B [auth A] Focus chain D [auth B] Focus chain F [auth C] Focus chain H [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C]	I [auth C], J [auth C], K [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.216 (Depositor), 0.180 (DCC)
R-Value Work: 0.180 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.086	α = 90
b = 9.826	β = 92.32
c = 35.093	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-23
Type: Initial release
Version 1.1: 2022-03-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-02-28
Changes: Data collection
Version 1.3: 2024-03-13
Changes: Source and taxonomy, Structure summary