4Y49

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

PDB DOI: https://doi.org/10.2210/pdb4Y49/pdb

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

Deposited: 2015-02-10 Released: 2016-07-13
Deposition Author(s): Dong, J., Wang, S., York, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.95 Å
R-Value Free: 0.421
R-Value Work: 0.355
R-Value Observed: 0.358

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 yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate

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

To be published.

Macromolecule Content

Total Structure Weight: 449.31 kDa
Atom Count: 20,122
Modelled Residue Count: 3,283
Deposited Residue Count: 3,828
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex subunit NAT1	A, E [auth G], I [auth M]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12945
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex catalytic subunit ARD1	B, F [auth H], J [auth N]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07347
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase A complex subunit NAT5	C, G [auth I], K [auth O]	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
ALA-ALA-ALA-ALA-ALA-ALA	D [auth E], H [auth K], L [auth Q]	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 N [auth B] SDF format, chain Q [auth H] SDF format, chain T [auth N] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth H] MOL2 format, chain T [auth N] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth H] mmCIF format, chain T [auth N]	N [auth B], Q [auth H], T [auth N]	*CARBOXYMETHYL COENZYME A** C₂₃ H₃₈ N₇ O₁₈ P₃ S OBUOSIHPWVNVJN-GRFIIANRSA-N		Interactions Focus chain N [auth B] Focus chain Q [auth H] Focus chain T [auth N] Interactions & Density Focus chain N [auth B] Focus chain Q [auth H] Focus chain T [auth N]
ACO Query on ACO Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain R [auth I] SDF format, chain U [auth O] MOL2 format, chain O [auth C] MOL2 format, chain R [auth I] MOL2 format, chain U [auth O] mmCIF format, chain O [auth C] mmCIF format, chain R [auth I] mmCIF format, chain U [auth O]	O [auth C], R [auth I], U [auth O]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain O [auth C] Focus chain R [auth I] Focus chain U [auth O] Interactions & Density Focus chain O [auth C] Focus chain R [auth I] Focus chain U [auth O]
G4P Query on G4P Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain P [auth G] SDF format, chain S [auth M] MOL2 format, chain M [auth A] MOL2 format, chain P [auth G] MOL2 format, chain S [auth M] mmCIF format, chain M [auth A] mmCIF format, chain P [auth G] mmCIF format, chain S [auth M]	M [auth A], P [auth G], S [auth M]	GUANOSINE-5',3'-TETRAPHOSPHATE C₁₀ H₁₇ N₅ O₁₇ P₄ BUFLLCUFNHESEH-UUOKFMHZSA-N		Interactions Focus chain M [auth A] Focus chain P [auth G] Focus chain S [auth M] Interactions & Density Focus chain M [auth A] Focus chain P [auth G] Focus chain S [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.95 Å
R-Value Free: 0.421
R-Value Work: 0.355
R-Value Observed: 0.358
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.723	α = 90
b = 146.486	β = 90
c = 254.107	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-07-13

Deposition Author(s):

Dong, J.

Wang, S.

York, J.D.

Revision History (Full details and data files)

Version 1.0: 2016-07-13
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Structure summary