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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF FDTS FROM T. MARITIMA MUTANT (H53D) WITH FAD AND DUMP

Authors :   I. I. Mathews

Date :   22 Apr 13 (Deposition) - 26 Mar 14 (Release) - 26 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Thyx, Fdts, Fad, Dump, Novel Fdts Fold, Convertion Of Dump To Dtmp Using Tetrahydrofolate, And Nad(P)Hc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. I. Mathews
Flavin-Dependent Thymidylate Synthase As A Drug Target For Deadly Microbes: Mutational Study And A Strategy For Inhibitor Design.
J Bioterror Biodef V. L 12 004 2013
PubMed-ID: 24563811 | Reference-DOI: 10.4172/2157-2526.S12-004

Molecule 1 - THYMIDYLATE SYNTHASE THYX
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.148
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMH1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TM0449 (UNP RESIDUES 1-220)
	Gene	:	THY1, THYX, TM0449, TM_0449
	Mutation	:	YES
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
	Synonym	:	TS, TSASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 10)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	CL	1	Ligand/Ion	CHLORIDE ION
3	DU	3	Ligand/Ion	2'-DEOXYURIDINE-5'-MONOPHOSPHATE
4	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
5	PO4	1	Ligand/Ion	PHOSPHATE ION
6	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:86 , LEU A:87 , SER A:88 , GLY A:89 , ARG A:90 , ARG A:147 , HOH A:408 , HOH A:417 , HOH A:449 , ARG D:74 , GLN D:75 , ARG D:78 , ARG D:174 , FAD D:301	BINDING SITE FOR RESIDUE DU A 301
02	AC2	SOFTWARE	ARG A:78 , HIS A:79 , ARG A:80 , ILE A:81 , ASN A:169	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	GLU B:86 , LEU B:87 , SER B:88 , GLY B:89 , ARG B:90 , ARG B:147 , HOH B:406 , HOH B:407 , ARG C:74 , GLN C:75 , ARG C:78 , ARG C:174 , FAD C:301	BINDING SITE FOR RESIDUE DU B 301
04	AC4	SOFTWARE	ARG B:78 , HIS B:79 , ARG B:80 , ILE B:81 , ASN B:169	BINDING SITE FOR RESIDUE SO4 B 302
05	AC5	SOFTWARE	SER A:30 , THR A:55 , GLU A:58 , ILE A:81 , ASN A:163 , ARG A:165 , SER A:166 , ASN B:85 , GLU B:86 , SER B:88 , TYR B:91 , DU B:301 , ARG C:78 , HIS C:79 , ARG C:80 , ILE C:81 , ASN C:169 , LEU C:173 , HIS C:178 , HOH C:403 , HOH C:405 , HOH C:407 , HOH C:488	BINDING SITE FOR RESIDUE FAD C 301
06	AC6	SOFTWARE	GLN B:75 , ARG B:78 , ARG B:174 , GLU C:86 , LEU C:87 , SER C:88 , GLY C:89 , ARG C:90 , ARG C:147 , HOH C:409 , HOH C:413	BINDING SITE FOR RESIDUE DU C 302
07	AC7	SOFTWARE	TYR C:208	BINDING SITE FOR RESIDUE CL C 303
08	AC8	SOFTWARE	SER A:83 , ASN A:85 , GLU A:86 , TYR A:91 , DU A:301 , SER B:30 , ASP B:53 , THR B:55 , GLU B:58 , ILE B:81 , ASN B:163 , ARG B:165 , ASN B:169 , ARG D:78 , HIS D:79 , ARG D:80 , ILE D:81 , ASN D:169 , LEU D:173 , ARG D:174 , HIS D:178 , HOH D:406 , HOH D:415 , HOH D:450 , HOH D:468	BINDING SITE FOR RESIDUE FAD D 301
09	AC9	SOFTWARE	GLN A:75 , HOH A:435 , ARG D:147 , HOH D:451 , HOH D:470	BINDING SITE FOR RESIDUE PO4 D 302
10	BC1	SOFTWARE	GLU C:203 , LEU C:215 , LYS C:216 , GLN C:219 , HIS D:43 , GLU D:46 , LYS D:50	BINDING SITE FOR RESIDUE 2PE D 303

(no "SS Bond" information available for 4KAS)

(no "Cis Peptide Bond" information available for 4KAS)

(no "SAP(SNP)/Variant" information available for 4KAS)

(no "PROSITE Motif" information available for 4KAS)

(no "Exon" information available for 4KAS)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4kasa_ A: Thy1 homologue                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeeeee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kas A  -1 HHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDDEERDRHLIEYLMKHGDETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
                                     8        18        28   ||   42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
                                                            32|                                                                                                                                                                                  
                                                             37

Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d4kasb_ B: Thy1 homologue                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeeeee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kas B   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDDEERDRHLIEYLMKHGDETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                                     9        19        29  ||    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       
                                                           32|                                                                                                                                                                                       
                                                            37

Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d4kasc_ C: Thy1 homologue                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeeeee.hhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kas C   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDKDEERDRHLIEYLMKHGDETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                                     9        19        29  ||    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
                                                           32|                                                                                                                                                                                        
                                                            36

Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4kasd_ D: Thy1 homologue                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kas D   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDKDEERDRHLIEYLMKHGDETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKE 217
                                    10        20        30 ||     43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
                                                          32|                                                                                                                                                                                     
                                                           36

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Thymidylate synthase-complementing protein Thy1 (24)

Superfamily: Thymidylate synthase-complementing protein Thy1 (24)

Family: Thymidylate synthase-complementing protein Thy1 (24)

Protein domain: Thy1 homologue (22)

Thermotoga maritima [TaxId: 2336] (22)

1a	d4kasa_	A:
1b	d4kasb_	B:
1c	d4kasc_	C:
1d	d4kasd_	D:

(no "CATH Domain" information available for 4KAS)

(no "Pfam Domain" information available for 4KAS)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4kas)

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Access by PDB/NDB ID
	4kas
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
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Access by UniProt ID/Accession number
	THYX_THEMA \| Q9WYT0
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	2.1.1.148
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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