2WK5 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURAL FEATURES OF NATIVE HUMAN THYMIDINE PHOSPHORYLASE AND IN COMPLEX WITH 5-IODOURACIL

Authors :   E. Mitsiki, A. C. Papageorgiou, S. Iyer, N. Thiyagarajan, S. H. Prior, D. Sleep, C. Finnis, K. R. Acharya

Date :   05 Jun 09 (Deposition) - 07 Jul 09 (Release) - 28 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.99

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Glycosyltransferase, Developmental Protein, Angiogenesis, 5-Iodouracil, Growth Factor, Enzyme Kinetics, Differentiation, Disease Mutation, Thymidine Phosphorylase, Chemotaxis, Transferase, Mutagenesis, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Mitsiki, A. C. Papageorgiou, S. Iyer, N. Thiyagarajan, S. H. Prior, D. Sleep, C. Finnis, K. R. Acharya
Structures Of Native Human Thymidine Phosphorylase And In Complex With 5-Iodouracil.
Biochem. Biophys. Res. Commun. V. 386 666 2009
PubMed-ID: 19555658 | Reference-DOI: 10.1016/J.BBRC.2009.06.104

Molecule 1 - THYMIDINE PHOSPHORYLASE
	Chains	:	A, B, C, D
	EC Number	:	2.4.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PYSBLIC
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIPL
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TDRPASE, PLATELET-DERIVED ENDOTHELIAL CELL GROWTH FACTOR, GLIOSTATIN, TP, PD-ECGF

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:304 , HOH B:2006 , HOH B:2007	BINDING SITE FOR RESIDUE GOL B1481

(no "SS Bond" information available for 2WK5)

(no "Cis Peptide Bond" information available for 2WK5)

Asymmetric Unit (6, 24)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016777	R	44	Q	TYPH_HUMAN	Disease (MTDPS1)	28931613	A/B/C/D	R	44	Q
2	UniProt	VAR_007643	G	145	R	TYPH_HUMAN	Disease (MTDPS1)	121913037	A/B/C/D	G	145	R
3	UniProt	VAR_007644	G	153	S	TYPH_HUMAN	Disease (MTDPS1)	121913038	A/B/C/D	G	153	S
4	UniProt	VAR_007645	K	222	R	TYPH_HUMAN	Disease (MTDPS1)	149977726	A/B/C/D	K	222	R
5	UniProt	VAR_007646	E	289	A	TYPH_HUMAN	Disease (MTDPS1)	121913036	A/B/C/D	E	289	A
6	UniProt	VAR_007648	S	471	L	TYPH_HUMAN	Polymorphism	11479	A/B/C/D	S	471	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016777	R	44	Q	TYPH_HUMAN	Disease (MTDPS1)	28931613	A	R	44	Q
2	UniProt	VAR_007643	G	145	R	TYPH_HUMAN	Disease (MTDPS1)	121913037	A	G	145	R
3	UniProt	VAR_007644	G	153	S	TYPH_HUMAN	Disease (MTDPS1)	121913038	A	G	153	S
4	UniProt	VAR_007645	K	222	R	TYPH_HUMAN	Disease (MTDPS1)	149977726	A	K	222	R
5	UniProt	VAR_007646	E	289	A	TYPH_HUMAN	Disease (MTDPS1)	121913036	A	E	289	A
6	UniProt	VAR_007648	S	471	L	TYPH_HUMAN	Polymorphism	11479	A	S	471	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016777	R	44	Q	TYPH_HUMAN	Disease (MTDPS1)	28931613	B	R	44	Q
2	UniProt	VAR_007643	G	145	R	TYPH_HUMAN	Disease (MTDPS1)	121913037	B	G	145	R
3	UniProt	VAR_007644	G	153	S	TYPH_HUMAN	Disease (MTDPS1)	121913038	B	G	153	S
4	UniProt	VAR_007645	K	222	R	TYPH_HUMAN	Disease (MTDPS1)	149977726	B	K	222	R
5	UniProt	VAR_007646	E	289	A	TYPH_HUMAN	Disease (MTDPS1)	121913036	B	E	289	A
6	UniProt	VAR_007648	S	471	L	TYPH_HUMAN	Polymorphism	11479	B	S	471	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016777	R	44	Q	TYPH_HUMAN	Disease (MTDPS1)	28931613	C	R	44	Q
2	UniProt	VAR_007643	G	145	R	TYPH_HUMAN	Disease (MTDPS1)	121913037	C	G	145	R
3	UniProt	VAR_007644	G	153	S	TYPH_HUMAN	Disease (MTDPS1)	121913038	C	G	153	S
4	UniProt	VAR_007645	K	222	R	TYPH_HUMAN	Disease (MTDPS1)	149977726	C	K	222	R
5	UniProt	VAR_007646	E	289	A	TYPH_HUMAN	Disease (MTDPS1)	121913036	C	E	289	A
6	UniProt	VAR_007648	S	471	L	TYPH_HUMAN	Polymorphism	11479	C	S	471	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016777	R	44	Q	TYPH_HUMAN	Disease (MTDPS1)	28931613	D	R	44	Q
2	UniProt	VAR_007643	G	145	R	TYPH_HUMAN	Disease (MTDPS1)	121913037	D	G	145	R
3	UniProt	VAR_007644	G	153	S	TYPH_HUMAN	Disease (MTDPS1)	121913038	D	G	153	S
4	UniProt	VAR_007645	K	222	R	TYPH_HUMAN	Disease (MTDPS1)	149977726	D	K	222	R
5	UniProt	VAR_007646	E	289	A	TYPH_HUMAN	Disease (MTDPS1)	121913036	D	E	289	A
6	UniProt	VAR_007648	S	471	L	TYPH_HUMAN	Polymorphism	11479	D	S	471	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMID_PHOSPHORYLASE	PS00647	Thymidine and pyrimidine-nucleoside phosphorylases signature.	TYPH_HUMAN	144-159	4	A:144-159 B:144-159 C:144-159 D:144-159

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMID_PHOSPHORYLASE	PS00647	Thymidine and pyrimidine-nucleoside phosphorylases signature.	TYPH_HUMAN	144-159	1	A:144-159 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMID_PHOSPHORYLASE	PS00647	Thymidine and pyrimidine-nucleoside phosphorylases signature.	TYPH_HUMAN	144-159	1	- B:144-159 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMID_PHOSPHORYLASE	PS00647	Thymidine and pyrimidine-nucleoside phosphorylases signature.	TYPH_HUMAN	144-159	1	- - C:144-159 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMID_PHOSPHORYLASE	PS00647	Thymidine and pyrimidine-nucleoside phosphorylases signature.	TYPH_HUMAN	144-159	1	- - - D:144-159

Asymmetric Unit (9, 36)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1g	ENST00000395680	1g	ENSE00001522468	chr22:50968428-50968333	96	TYPH_HUMAN	-	0	0	-	-
1.1j	ENST00000395680	1j	ENSE00001522466	chr22:50968183-50967925	259	TYPH_HUMAN	1-72	72	4	A:32-72 B:32-72 C:33-72 D:34-72	41 41 40 39
1.1o	ENST00000395680	1o	ENSE00000657761	chr22:50967767-50967565	203	TYPH_HUMAN	72-139	68	4	A:72-139 B:72-139 (gaps) C:72-139 D:72-139 (gaps)	68 68 68 68
1.1p	ENST00000395680	1p	ENSE00000657760	chr22:50967039-50966941	99	TYPH_HUMAN	140-172	33	4	A:140-172 B:140-172 C:140-172 D:140-172	33 33 33 33
1.2a	ENST00000395680	2a	ENSE00000657759	chr22:50966146-50966017	130	TYPH_HUMAN	173-216	44	4	A:173-216 B:173-216 C:173-216 D:173-216	44 44 44 44
1.3	ENST00000395680	3	ENSE00000878932	chr22:50965712-50965594	119	TYPH_HUMAN	216-255	40	4	A:216-255 B:216-255 C:216-255 D:216-255	40 40 40 40
1.4	ENST00000395680	4	ENSE00000657757	chr22:50965167-50965005	163	TYPH_HUMAN	256-310	55	4	A:256-310 B:256-310 C:256-310 D:256-310	55 55 55 55
1.5a	ENST00000395680	5a	ENSE00000657756	chr22:50964905-50964675	231	TYPH_HUMAN	310-387	78	4	A:310-387 B:310-387 C:310-387 D:310-387 (gaps)	78 78 78 78
1.5d	ENST00000395680	5d	ENSE00000657754	chr22:50964570-50964430	141	TYPH_HUMAN	387-434	48	4	A:387-434 B:387-434 C:387-434 D:387-434	48 48 48 48
1.6e	ENST00000395680	6e	ENSE00000878931	chr22:50964347-50964181	167	TYPH_HUMAN	434-482	49	4	A:434-480 B:434-481 C:434-480 (gaps) D:434-480	47 48 47 47

Asymmetric 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:449
 aligned with TYPH_HUMAN | P19971 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:449
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471         
           TYPH_HUMAN    32 EPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP 480
               SCOP domains d2wk5a1 A:32-100 automated matches                                   d2wk5a2 A:101-373 automated matches                                                                                                                                                                                                                                              d2wk5a3 A:374-480 automated matches                                                                         SCOP domains
               CATH domains 2wk5A01 A:32-100                                                     2wk5A02 A:101-371,A:468-480 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                                                                                                                                             2wk5A03 A:372-467  [code=3.90.1170.30, no name defined]                                         2wk5A02       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhh.eeee........hhhhhhhhhhhh...eeeee........hhhhhhh.........hhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhh..eeeeeee.......ee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeehhhhhhhhhhhh...............eeee......ee....eeeeeee.....hhhhhhhhhh.eeee..........eeeee... Sec.struct. author
                 SAPs(SNPs) ------------Q----------------------------------------------------------------------------------------------------R-------S--------------------------------------------------------------------R------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L--------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1j  PDB: A:32-72 UniProt: 1-72    -------------------------------------------------------------------Exon 1.1p  PDB: A:140-172        Exon 1.2a  PDB: A:173-216 UniProt: 173-216  ---------------------------------------Exon 1.4  PDB: A:256-310 UniProt: 256-310              ----------------------------------------------------------------------------Exon 1.5d  PDB: A:387-434 UniProt: 387-434      ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.1o  PDB: A:72-139 UniProt: 72-139                            ----------------------------------------------------------------------------Exon 1.3  PDB: A:216-255                ------------------------------------------------------Exon 1.5a  PDB: A:310-387 UniProt: 310-387                                    ----------------------------------------------Exon 1.6e  PDB: A:434-480 UniProt: 434-482      Transcript 1 (2)
                 2wk5 A  32 EPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP 480
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471

Chain B from PDB  Type:PROTEIN  Length:448
 aligned with TYPH_HUMAN | P19971 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:450
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
           TYPH_HUMAN    32 EPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPPQ 481
               SCOP domains d2wk5b1 B:32-100 automated matches                                   d2wk5  b2 B:101-373 automated matches                                                                                                                                                                                                                                            d2wk5b3 B:374-481 automated matches                                                                          SCOP domains
               CATH domains 2wk5B01 B:32-100                                                     2wk5B  02 B:101-371,B:468-481 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                                                                                                                                           2wk5B03 B:372-467  [code=3.90.1170.30, no name defined]                                         2wk5B02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........--.....eeeee......hhhhhhhhhhh.....eeee.........hhhhhhh.........hhhhhhhhhhhh.eeee......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeeee.......eee..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhh....eeeeee....eeeeeehhhhhhhhhhhh...............eeee......ee....eeeeeee.....hhhhhhhhhhheeee..........eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------Q----------------------------------------------------------------------------------------------------R-------S--------------------------------------------------------------------R------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L---------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1j  PDB: B:32-72 UniProt: 1-72    -------------------------------------------------------------------Exon 1.1p  PDB: B:140-172        Exon 1.2a  PDB: B:173-216 UniProt: 173-216  ---------------------------------------Exon 1.4  PDB: B:256-310 UniProt: 256-310              ----------------------------------------------------------------------------Exon 1.5d  PDB: B:387-434 UniProt: 387-434      ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.1o  PDB: B:72-139 (gaps) UniProt: 72-139                     ----------------------------------------------------------------------------Exon 1.3  PDB: B:216-255                ------------------------------------------------------Exon 1.5a  PDB: B:310-387 UniProt: 310-387                                    ----------------------------------------------Exon 1.6e  PDB: B:434-481 UniProt: 434-482       Transcript 1 (2)
                 2wk5 B  32 EPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWP--WRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPPQ 481
                                    41        51        61        71        81        91       101   |  |111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
                                                                                                   105  |                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                      108

Chain C from PDB  Type:PROTEIN  Length:445
 aligned with TYPH_HUMAN | P19971 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:448
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472        
           TYPH_HUMAN    33 PKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP 480
               SCOP domains d2wk5c1 C:33-100 automated matches                                  d2wk5c2 C:101-373 automated matches                                                                                                                                                                                                                                              d2wk5c3 C:374-480 automated matches                                                                         SCOP domains
               CATH domains 2wk5C01 C:33-100                                                    2wk5C02 C:101-371,C:469-480 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                                                                                                                                             2wk5C03 C:372-465  [code=3.90.1170.30, no name defined]                                       ---2wk5C02      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.................eee......hhhhhhhhhhhh....eeee.........hhhhhhhh..........hhhhhhhhhh.eeee......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhhhhh......eeee.......eeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....eee.......eeeeeehhhhhhhhhhh................eeee......ee......eeeee.....hhhhhhhhhh.eeee...---....eee..... Sec.struct. author
                 SAPs(SNPs) -----------Q----------------------------------------------------------------------------------------------------R-------S--------------------------------------------------------------------R------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L--------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1j  PDB: C:33-72 UniProt: 1-72   -------------------------------------------------------------------Exon 1.1p  PDB: C:140-172        Exon 1.2a  PDB: C:173-216 UniProt: 173-216  ---------------------------------------Exon 1.4  PDB: C:256-310 UniProt: 256-310              ----------------------------------------------------------------------------Exon 1.5d  PDB: C:387-434 UniProt: 387-434      ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.1o  PDB: C:72-139 UniProt: 72-139                            ----------------------------------------------------------------------------Exon 1.3  PDB: C:216-255                ------------------------------------------------------Exon 1.5a  PDB: C:310-387 UniProt: 310-387                                    ----------------------------------------------Exon 1.6e  PDB: C:434-480 (gaps) [INCOMPLETE]   Transcript 1 (2)
                 2wk5 C  33 PKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRA---APSPFAELVLPP 480
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462  |   |472        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          465 469

Chain D from PDB  Type:PROTEIN  Length:445
 aligned with TYPH_HUMAN | P19971 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:447
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       
           TYPH_HUMAN    34 KQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP 480
               SCOP domains d2wk5d1 D:34-100 automated matches                                 d 2wk5d2 D:101-373 automated matches                                                                                                                                                                                                                                             d2wk5d3 D:374-480 automated matches                                                                         SCOP domains
               CATH domains 2wk5D01 D:34-100                                                   2 wk5D02 D:101-371,D:468-480 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                                                                                                                                            2wk5D03 D:372-467  [code=3.90.1170.30, no name defined]                                         2wk5D02       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....-..hhhhh...eeeee......hhhhhhhhhhhhh...eeee.........hhhhhhh...........hhhhhhh....eeee......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhhhh.....eeeee.......eeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh-....hhhhhh....eeeeee....eeeeeehhhhhhhhhhhh...............eeee......ee....eeeeeee.....hhhhhhhhhhheeee..........eeeee... Sec.struct. author
                 SAPs(SNPs) ----------Q----------------------------------------------------------------------------------------------------R-------S--------------------------------------------------------------------R------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L--------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1j  PDB: D:34-72 UniProt: 1-72  -------------------------------------------------------------------Exon 1.1p  PDB: D:140-172        Exon 1.2a  PDB: D:173-216 UniProt: 173-216  ---------------------------------------Exon 1.4  PDB: D:256-310 UniProt: 256-310              ----------------------------------------------------------------------------Exon 1.5d  PDB: D:387-434 UniProt: 387-434      ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.1o  PDB: D:72-139 (gaps) UniProt: 72-139                     ----------------------------------------------------------------------------Exon 1.3  PDB: D:216-255                ------------------------------------------------------Exon 1.5a  PDB: D:310-387 (gaps) UniProt: 310-387                             ----------------------------------------------Exon 1.6e  PDB: D:434-480 UniProt: 434-482      Transcript 1 (2)
                 2wk5 D  34 KQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQ-EWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALC-GSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP 480
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       
                                                                                             101 |                                                                                                                                                                                                                                                               361 |                                                                                                                     
                                                                                               103                                                                                                                                                                                                                                                                 363

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 (23)

Homologous Superfamily: Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 (23)

Human (Homo sapiens) (4)

1a	2wk5D02	D:101-371,D:468-480
1b	2wk5A02	A:101-371,A:468-480
1c	2wk5B02	B:101-371,B:468-481
1d	2wk5C02	C:101-371,C:469-480

Architecture: Alpha-Beta Complex (3881)

Topology: Aldehyde Oxidoreductase; domain 3 (111)

Homologous Superfamily: [code=3.90.1170.30, no name defined] (10)

Human (Homo sapiens) (4)

2a	2wk5A03	A:372-467
2b	2wk5C03	C:372-465
2c	2wk5B03	B:372-467
2d	2wk5D03	D:372-467

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 (19)

Homologous Superfamily: Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C (18)

Human (Homo sapiens) (4)

3a	2wk5A01	A:32-100
3b	2wk5D01	D:34-100
3c	2wk5B01	B:32-100
3d	2wk5C01	C:33-100

(no "Pfam Domain" information available for 2WK5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TYPH_HUMAN | P19971)

molecular function
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0004645	phosphorylase activity	Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate. The name should be qualified in each instance by adding the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase.
	GO:0005161	platelet-derived growth factor receptor binding	Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
	GO:0016154	pyrimidine-nucleoside phosphorylase activity	Catalysis of the reaction: pyrimidine nucleoside + phosphate = pyrimidine + alpha-D-ribose 1-phosphate.
	GO:0009032	thymidine phosphorylase activity	Catalysis of the reaction: thymidine + phosphate = thymine + 2-deoxy-D-ribose 1-phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
	GO:0016763	transferase activity, transferring pentosyl groups	Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0000002	mitochondrial genome maintenance	The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0006206	pyrimidine nucleobase metabolic process	The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
	GO:0046135	pyrimidine nucleoside catabolic process	The chemical reactions and pathways resulting in the breakdown of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
	GO:0006213	pyrimidine nucleoside metabolic process	The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
	GO:0043097	pyrimidine nucleoside salvage	Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	TYPH_HUMAN \| P19971
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	TYPH_HUMAN \| P19971	:	1uou 2j0f 2wk6

1uou	CRYSTAL STRUCTURE OF HUMAN THYMIDINE PHOSPHORYLASE IN COMPLEX WITH A SMALL MOLECULE INHIBITOR
2j0f	STRUCTURAL BASIS FOR NON-COMPETITIVE PRODUCT INHIBITION IN HUMAN THYMIDINE PHOSPHORYLASE: IMPLICATION FOR DRUG DESIGN
2wk6	STRUCTURAL FEATURES OF NATIVE HUMAN THYMIDINE PHOSPHORYLASE AND IN COMPLEX WITH 5- IODOURACIL

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

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SAPs(SNPs)/Variants (6, 24)

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Exons (9, 36)

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