6VFD | pdb_00006vfd

Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site

PDB DOI: https://doi.org/10.2210/pdb6VFD/pdb

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

Deposited: 2020-01-03 Released: 2020-08-05
Deposition Author(s): Hilario, E., Fan, L., Dunn, M.F., Mueller, L.J.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.224 (Depositor), 0.223 (DCC)
R-Value Work:
0.195 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (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

Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site.

Hilario, E., Fan, L., Dunn, M.F., Mueller, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 74.19 kDa
Atom Count: 5,908
Modeled Residue Count: 648
Deposited Residue Count: 665
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A	268	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: trpA, DD95_04145 EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P00929 Go to UniProtKB: P00929
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00929
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B	397	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 1 Gene Names: trpB, AAP89_02045, ABO94_19170, AF480_03975, AF488_06015, AF489_02660, AIC76_02215, AU613_22485, AXR84_21850, AXU58_18720... trpB, AAP89_02045, ABO94_19170, AF480_03975, AF488_06015, AF489_02660, AIC76_02215, AU613_22485, AXR84_21850, AXU58_18720, C2253_17845, CD48_01255, CE87_00490, CET98_00490, CQG18_02715, CVR97_02985, D4369_03495, D4380_02480, D4401_03780, D4E62_00155, D6360_05135, D7F20_01770, D7H43_22440, DD95_04150, DJ388_09100, DKJ11_03255, DKU57_01740, DLM31_00170, DNV30_02640, DO698_02865, DOJ90_01720, DOQ88_05395, DQ848_22185, DRM14_00170, DSF69_00170, DSR36_00155, DUW48_00170, E2F01_02625, EBO41_01950, EBP31_03920, EGU67_04975, EHB24_02705, EHC98_05585, EIW53_01745, F0A00_14785, F0A01_15745, F0A02_08960, F0A03_20195, F0A04_22070, F0A05_01740, F0A06_01905, F0A07_12870, F0A08_01425, F0U66_12100, FKA80_16460, FKA81_16995, FKA82_17080, FKA83_17705, FKA84_18900, FKA85_16755, FKA86_15095, FKA87_20420, FKA88_00465, FKA89_17495, FKA90_04050, FKA91_03380, FKA92_00475, FKA93_04425, FKA94_02440, FKA95_00475, FKA96_03185, FKA97_05420, FKA98_04655, FKA99_00465, FKB00_08210, FKB01_00475, FKB02_00470, FKB03_06095, FKB12_08200, FKB15_09545, FKB19_17260, FYL57_17810, FYL66_01025, FYL68_08225, FYL69_04355, FYL71_20365, FYL73_06975, FYL74_10415, FYL75_12085, FYL77_17200, FYL81_18315, FYL84_11395, FYL90_05690, FYL92_04810, FYL93_03130, FYL94_11585, FYL96_18520, FYM06_17485, FYM08_08630, FYM09_19335, FYM12_03600, FYM54_08665, FZ992_19115, FZ993_02220, FZ994_08290, FZ995_12310, FZ996_09230, FZ997_15170, FZ998_14625, FZ999_17455, GW08_03175, JO10_00490, LZ63_02660, NG18_14010, NU83_02660, QA89_14465, QB40_00170, QD15_05225, RJ78_16500, SAMEA4398682_02247, UPM260_1493, Y934_00965, YG50_13195, YI33_00155, YR17_00170, YT65_03520, ZA53_18735, ZB89_05455, ZC54_00170 EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2K1 Go to UniProtKB: P0A2K1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A2K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1D0 (Subject of Investigation/LOI) Query on 1D0 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid C₁₇ H₂₀ N₃ O₈ P MKNJFLJOSVXALN-XMHGGMMESA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
CS Query on CS Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B]	V [auth B], W [auth B], X [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
SER Query on SER Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A] M [auth B] N [auth B] O [auth B] P [auth B] F [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain Y [auth B] Focus chain Z [auth B]