7I08 | pdb_00007i08

PanDDA analysis group deposition -- Crystal structure of Enterococcus faecium VatD in complex with ZINC000004976927

PDB DOI: https://doi.org/10.2210/pdb7I08/pdb
Deposition Group: G_1002332 (changed state) ExploreG_1002332

Classification: TRANSFERASE
Organism(s): Enterococcus faecium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-25 Released: 2026-01-28
Deposition Author(s): Asthana, P., Fraser, J.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.306 (Depositor), 0.306 (DCC)
R-Value Work:
0.237 (Depositor), 0.246 (DCC)
R-Value Observed:
0.240 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Ligand screen against Enterococcus faecium VatD

Asthana, P., Fraser, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 71.3 kDa
Atom Count: 5,761
Modeled Residue Count: 608
Deposited Residue Count: 627
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptogramin A acetyltransferase	A, B, C	209	Enterococcus faecium	Mutation(s): 0 Gene Names: vatD, satA EC: 2.3.1
UniProt
Find proteins for P50870 (Enterococcus faecium) Explore P50870 Go to UniProtKB: P50870
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50870
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
04R Query on 04R Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain D [auth A] MOL2 format, chain E [auth C] MOL2 format, chain D [auth A] mmCIF format, chain E [auth C] mmCIF format, chain D [auth A]	D [auth A], E [auth C]	[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetic acid C₁₀ H₁₁ F₃ N₂ O₂ NOFFCWXIBYKMBU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.306 (Depositor), 0.306 (DCC)
R-Value Work: 0.237 (Depositor), 0.246 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.149	α = 90
b = 102.333	β = 90
c = 146.297	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM145238

Revision History (Full details and data files)

Version 1.0: 2026-01-28
Type: Initial release

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.