2PSW

Human MAK3 homolog in complex with CoA

PDB DOI: https://doi.org/10.2210/pdb2PSW/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-05-07 Released: 2007-06-05
Deposition Author(s): Walker, J.R., Schuetz, A., Antoshenko, T., Wu, H., Bernstein, G., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.265
R-Value Work: 0.197
R-Value Observed: 0.201

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Structure of Human MAK3 homolog.

Schuetz, A., Walker, J.R., Antoshenko, T., Wu, H., Bernstein, G., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 60.9 kDa
Atom Count: 3,995
Modelled Residue Count: 459
Deposited Residue Count: 510
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyltransferase 13	A, B, C	170	Homo sapiens	Mutation(s): 2 Gene Names: NAT13, MAK3, NAT5 EC: 2.3.1.88 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.258 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZZ1 (Homo sapiens) Explore Q9GZZ1 Go to UniProtKB: Q9GZZ1
PHAROS: Q9GZZ1 GTEx: ENSG00000121579
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GZZ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
COA	BindingDB: 2PSW	Kd: 156 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.265
R-Value Work: 0.197
R-Value Observed: 0.201
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.643	α = 90
b = 102.913	β = 105.81
c = 67.157	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
ARP/wARP	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-06-05
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-08-31
Changes: Atomic model
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-10-16
Changes: Structure summary