4JEX | pdb_00004jex

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 (Depositor), 0.170 (DCC)
R-Value Work:
0.156 (Depositor), 0.150 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
View more details

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

Find similar proteins by:

(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 LOADING

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 D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain X [auth B] SDF format, chain T [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth B] MOL2 format, chain T [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain X [auth B] mmCIF format, chain T [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 G [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain W [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain W [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 N [auth A] SDF format, chain Y [auth B] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain N [auth A] mmCIF format, chain Y [auth B]	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 (Depositor), 0.170 (DCC)
R-Value Work: 0.156 (Depositor), 0.150 (DCC)
R-Value Observed: 0.157 (Depositor)

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