6TOV | pdb_00006tov

Crystal Structure of Teicoplanin Aglycone

PDB DOI: https://doi.org/10.2210/pdb6TOV/pdb

Classification: ANTIBIOTIC
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2019-12-12 Released: 2020-01-15
Deposition Author(s): Belviso, B.D., Carrozzini, B., Caliandro, R., Altomare, C.D., Bolognino, I., Cellamare, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.77 Å
R-Value Free:
0.114 (Depositor), 0.119 (DCC)
R-Value Work:
0.097 (Depositor), 0.101 (DCC)
R-Value Observed:
0.097 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6TOV

This is version 1.1 of the entry. See complete history.

Literature

Enantiomeric Separation and Molecular Modelling of Bioactive 4-Aryl-3,4-dihydropyrimidin-2(1H)-one Ester Derivatives on Teicoplanin-Based Chiral Stationary Phase

Bolognino, I., Carrieri, A., Purgatorio, R., Catto, M., Caliandro, R., Carrozzini, B., Belviso, B.D., Majellaro, M., Sotelo, E., Cellamare, S., Altomare, C.D.

(2022) Separations

DOI: https://doi.org/10.3390/separations9010007

Macromolecule Content

Total Structure Weight: 1.6 kDa
Atom Count: 128
Modeled Residue Count: 7
Deposited Residue Count: 7
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Teicoplanin Aglycone	A	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3FG Query on 3FG	A	L-PEPTIDE LINKING	C₈ H₉ N O₄		--
3MY Query on 3MY	A	D-PEPTIDE LINKING	C₉ H₁₀ Cl N O₃		TYR
GHP Query on GHP	A	D-PEPTIDE LINKING	C₈ H₉ N O₃		--
OMY Query on OMY	A	L-PEPTIDE LINKING	C₉ H₁₀ Cl N O₄		TYR

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000210 Query on PRD_000210	A	Teicoplanin Aglycone	Oligopeptide / Antibiotic		Interactions Focus chain A Interactions & Density Focus chain A

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.77 Å
R-Value Free: 0.114 (Depositor), 0.119 (DCC)
R-Value Work: 0.097 (Depositor), 0.101 (DCC)
R-Value Observed: 0.097 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.722	α = 90
b = 13.113	β = 123.34
c = 21.717	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Sir2014	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2022-01-19
Changes: Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.