3DHO | pdb_00003dho

Structure of Streptogramin Acetyltransferase in Complex with an Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3DHO/pdb

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

Deposited: 2008-06-18 Released: 2009-09-22
Deposition Author(s): Roderick, S.L., Pesaresi, A., Wright, G.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.170 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of Streptogramin Acetyltransferase in Complex with an Inhibitor

Johnston, N.J., Blanchard, J.E., Koteva, K.P., Ejim, L.J., Pesaresi, A., Roderick, S.L., Wright, G.D.

To be published.

Macromolecule Content

Total Structure Weight: 145.65 kDa
Atom Count: 11,211
Modeled Residue Count: 1,218
Deposited Residue Count: 1,254
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptogramin A acetyltransferase	A, B, C, D, E A, B, C, D, E, F	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B2M Query on B2M Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E]	I [auth A] M [auth B] Q [auth C] U [auth D] X [auth E] I [auth A], M [auth B], Q [auth C], U [auth D], X [auth E], Y [auth E]	6-bromo-N'-[(1Z)-(3,5-dichloro-2-hydroxyphenyl)methylidene]-2-methylquinoline-4-carbohydrazide C₁₈ H₁₂ Br Cl₂ N₃ O₂ JOLMQMRBSITJES-UYOCIXKTSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth E]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] K [auth B] L [auth B] P [auth C] G [auth A], H [auth A], K [auth B], L [auth B], P [auth C], T [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain J [auth A] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Z [auth E] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain AA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain AA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	AA [auth F] J [auth A] N [auth B] O [auth B] R [auth C] AA [auth F], J [auth A], N [auth B], O [auth B], R [auth C], S [auth C], V [auth D], W [auth D], Z [auth E]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.170 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.653	α = 90
b = 183.62	β = 90
c = 183.644	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CTR	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-09-22

Deposition Author(s):

Roderick, S.L.

Pesaresi, A.

Wright, G.D.

Revision History (Full details and data files)

Version 1.0: 2009-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description