8DIL | pdb_00008dil

Crystal structure of putative nitroreductase from Salmonella enterica

PDB DOI: https://doi.org/10.2210/pdb8DIL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-29 Released: 2022-07-13
Deposition Author(s): Chang, C., Skarina, T., Mesa, N., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.274 (Depositor), 0.270 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.230 (Depositor)

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

Crystal structure of putative nitroreductase from Salmonella enterica

Chang, C., Skarina, T., Mesa, N., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 126.89 kDa
Atom Count: 9,441
Modeled Residue Count: 1,043
Deposited Residue Count: 1,098
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative NAD(P)H nitroreductase	A, B, C, D, E A, B, C, D, E, F	183	Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344	Mutation(s): 0 Gene Names: ydjA, SL1344_1231, G1W50_15780, G1W53_02785, G1W54_02785, G1W56_06140, G1W59_21080, G1W62_10980, G1W63_02785, G1W64_08545... ydjA, SL1344_1231, G1W50_15780, G1W53_02785, G1W54_02785, G1W56_06140, G1W59_21080, G1W62_10980, G1W63_02785, G1W64_08545, G1W67_10975, G1W72_21920, G1W73_21040, G1W84_21635, G1W85_21645, G1W86_02465, G1W87_16195, G1W89_05570, G1W92_14510, G1X00_22250, G1X03_02785, G1X04_04115, G1X09_05880, G1X10_02785, G1X11_22300, G1X12_22270, G1X13_05880, G1X15_08330, G1X17_05880, G1X18_22295, G1X19_16140, G1X23_02770, G1X29_05880, G1X31_22115, G1X32_05465, G1X38_02785, G1X42_14510, G1X44_10725, G1X46_21425, G1X47_05450, G1X49_02785, G1X50_08005, G1X51_05880, G1X52_08550, G1X57_14905, G1X61_10985, G1X64_10730, G1X66_02785, G1X67_10730, G1X68_02785, G1X69_06145, G1X71_05885, G1X76_02785, G1X80_02785, G1X84_05470, G1X85_02785, G1X86_16255, G1X87_08025, G1X94_05450, G1X96_16260, G1X98_22215, G1X99_08560, G1Y02_05470, G1Y04_10720, G1Y11_08890 EC: 1
UniProt
Find proteins for A0A0H3NAL3 (Salmonella typhimurium (strain SL1344)) Explore A0A0H3NAL3 Go to UniProtKB: A0A0H3NAL3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3NAL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain G [auth A] SDF format, chain IA [auth F] SDF format, chain L [auth B] SDF format, chain X [auth D] SDF format, chain Q [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain X [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain X [auth D] mmCIF format, chain Q [auth C]	CA [auth E] G [auth A] IA [auth F] L [auth B] Q [auth C] CA [auth E], G [auth A], IA [auth F], L [auth B], Q [auth C], X [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain CA [auth E] Focus chain G [auth A] Focus chain IA [auth F] Focus chain L [auth B] Focus chain Q [auth C] Focus chain X [auth D] Interactions & Density Focus chain CA [auth E] Focus chain G [auth A] Focus chain IA [auth F] Focus chain L [auth B] Focus chain Q [auth C] Focus chain X [auth D]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain Y [auth D] SDF format, chain JA [auth F] SDF format, chain H [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain JA [auth F] MOL2 format, chain H [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain JA [auth F] mmCIF format, chain H [auth A]	DA [auth E] H [auth A] JA [auth F] M [auth B] R [auth C] DA [auth E], H [auth A], JA [auth F], M [auth B], R [auth C], Y [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain H [auth A] Focus chain JA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain H [auth A] Focus chain JA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain Y [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain MA [auth F] SDF format, chain U [auth C] SDF format, chain Z [auth D] SDF format, chain I [auth A] MOL2 format, chain EA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain I [auth A] mmCIF format, chain EA [auth E] mmCIF format, chain MA [auth F] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain I [auth A]	EA [auth E], I [auth A], MA [auth F], U [auth C], Z [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain I [auth A] Focus chain MA [auth F] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain I [auth A] Focus chain MA [auth F] Focus chain U [auth C] Focus chain Z [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain LA [auth F] SDF format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain LA [auth F] MOL2 format, chain AA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain LA [auth F] mmCIF format, chain AA [auth D]	AA [auth D] FA [auth E] HA [auth E] K [auth A] KA [auth F] AA [auth D], FA [auth E], HA [auth E], K [auth A], KA [auth F], LA [auth F], S [auth C], T [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain HA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain HA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain S [auth C] Focus chain T [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain GA [auth E] SDF format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain GA [auth E] mmCIF format, chain BA [auth D]	BA [auth D] GA [auth E] J [auth A] N [auth B] O [auth B] BA [auth D], GA [auth E], J [auth A], N [auth B], O [auth B], P [auth B], V [auth C], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain W [auth C]