6VFD

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
R-Value Work: 0.195
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Currently 6VFD does not have a validation slider image.

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
Modelled Residue Count: 648
Deposited Residue Count: 665
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00929
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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 V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [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 E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B]	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 F [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain O [auth B] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth B]	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 K [auth B] SDF format, chain L [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [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 AA [auth B] SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [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]