4MY0

Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida

PDB DOI: https://doi.org/10.2210/pdb4MY0/pdb

Classification: TRANSFERASE
Organism(s): Kribbella flavida DSM 17836
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-09-26 Released: 2013-11-06
Deposition Author(s): Kim, Y., Mack, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.202
R-Value Work: 0.166
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida

Kim, Y., Mack, J., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 260.97 kDa
Atom Count: 18,874
Modelled Residue Count: 2,323
Deposited Residue Count: 2,352
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN5-related N-acetyltransferase	A, B, C, D, E A, B, C, D, E, F	392	Kribbella flavida DSM 17836	Mutation(s): 0 Gene Names: Kfla_4406
UniProt
Find proteins for D2PVF8 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PVF8 Go to UniProtKB: D2PVF8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2PVF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AC8 Query on AC8 Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-bis(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl dihydrogen diphosphate C₂₁ H₃₇ N₇ O₁₉ P₄ S SAXULFDJRFDTDN-IBOSZNHHSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
ACO Query on ACO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain S [auth F]	G [auth A], J [auth B], N [auth D], P [auth E], S [auth F]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth D] Focus chain P [auth E] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth D] Focus chain P [auth E] Focus chain S [auth F]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain T [auth F] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth F] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth F] mmCIF format, chain K [auth B]	H [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] H [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], T [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain T [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth E] MOL2 format, chain I [auth A] MOL2 format, chain R [auth E] mmCIF format, chain I [auth A] mmCIF format, chain R [auth E]	I [auth A], R [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth E] Interactions & Density Focus chain I [auth A] Focus chain R [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.202
R-Value Work: 0.166
R-Value Observed: 0.168
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.138	α = 90
b = 166.518	β = 90
c = 183.613	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-11-06
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary

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4MY0

Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida

Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)