4JEX

Y21K mutant of N-acetylornithine aminotransferase complexed with L-canaline

PDB DOI: https://doi.org/10.2210/pdb4JEX/pdb

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-02-27 Released: 2014-03-26
Deposition Author(s): Bisht, S., Bharath, S.R., Murthy, M.R.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.176
R-Value Work: 0.156
R-Value Observed: 0.157

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Conformational transitions, ligand specificity and catalysis in N-acetylornithine aminotransferase: Implications on drug designing and rational enzyme engineering in omega aminotransferases

Bisht, S., Bharath, S.R., Murthy, M.R.N.

To be published.

Macromolecule Content

Total Structure Weight: 93.56 kDa
Atom Count: 6,645
Modelled Residue Count: 761
Deposited Residue Count: 844
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylornithine/succinyldiaminopimelate aminotransferase	A, B	422	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 2 Gene Names: argD, dapC, dtu, STM3468 EC: 2.6.1.11 (PDB Primary Data), 2.6.1.17 (PDB Primary Data)
UniProt
Find proteins for P40732 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P40732 Go to UniProtKB: P40732
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40732
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P00 Query on P00 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Z [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain K [auth A] mmCIF format, chain Z [auth B]	K [auth A], Z [auth B]	(2S)-2-azanyl-4-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxy-butanoic acid C₁₂ H₁₈ N₃ O₈ P HDUKWWSNPJPYAB-XSFFOXFNSA-N		Interactions Focus chain K [auth A] Focus chain Z [auth B] Interactions & Density Focus chain K [auth A] Focus chain Z [auth B]
TNF Query on TNF Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	PICRIC ACID C₆ H₃ N₃ O₇ OXNIZHLAWKMVMX-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain T [auth B] SDF format, chain X [auth B] SDF format, chain D [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain X [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain T [auth B] mmCIF format, chain X [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B]	C [auth A] D [auth A] E [auth A] I [auth A] J [auth A] C [auth A], D [auth A], E [auth A], I [auth A], J [auth A], O [auth B], T [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth B] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth B] Focus chain X [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain W [auth B] SDF format, chain G [auth A] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain W [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth B]	F [auth A] G [auth A] H [auth A] L [auth A] M [auth A] F [auth A], G [auth A], H [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth B], W [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain W [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain W [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain N [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain N [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain N [auth A]	N [auth A], Y [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Y [auth B] Interactions & Density Focus chain N [auth A] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.176
R-Value Work: 0.156
R-Value Observed: 0.157
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.99	α = 90
b = 112.78	β = 90
c = 65.34	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Bisht, S.

Bharath, S.R.

Murthy, M.R.N.

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description