4XNH | pdb_00004xnh

Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a bisubstrate

PDB DOI: https://doi.org/10.2210/pdb4XNH/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-15 Released: 2016-07-20
Deposition Author(s): Dong, J., Wang, S., York, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.168 (Depositor), 0.173 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a bisubstrate

Dong, J., Wang, S., York, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 149.79 kDa
Atom Count: 10,132
Modeled Residue Count: 1,148
Deposited Residue Count: 1,276
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex subunit NAT1	A	854	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P12945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12945 Go to UniProtKB: P12945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12945
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex catalytic subunit ARD1	B	238	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.3.1.88 (PDB Primary Data), 2.3.1.255 (UniProt)
UniProt
Find proteins for P07347 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07347 Go to UniProtKB: P07347
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07347
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex subunit NAT5	C	176	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.3.1 (PDB Primary Data), 2.3.1.258 (UniProt)
UniProt
Find proteins for Q08689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08689 Go to UniProtKB: Q08689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08689
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYH8	D [auth F]	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01189 (Homo sapiens) Explore P01189 Go to UniProtKB: P01189
PHAROS: P01189 GTEx: ENSG00000115138
Entity Groups
UniProt Group	P01189
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CMC Query on CMC Download:Ideal Coordinates CCD File SDF format, chain G [auth F] MOL2 format, chain G [auth F] mmCIF format, chain G [auth F]	G [auth F]	*CARBOXYMETHYL COENZYME A** C₂₃ H₃₈ N₇ O₁₈ P₃ S OBUOSIHPWVNVJN-GRFIIANRSA-N		Interactions Focus chain G [auth F] Interactions & Density Focus chain G [auth F]
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
IHP Query on IHP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.168 (Depositor), 0.173 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.475	α = 90
b = 114.515	β = 90
c = 146.978	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Dong, J.

Wang, S.

York, J.D.

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 2.0: 2020-10-14
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-02-28
Changes: Data collection, Database references