1RYZ - 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 :   URIDINE PHOSPHORYLASE FROM SALMONELLA TYPHIMURIUM. CRYSTAL STRUCTURE AT 2.9 A RESOLUTION

Authors :   M. V. Dontsova, A. G. Gabdoulkhakov, A. V. Lyashenko, S. V. Nikonov, S. E A. M. Mikhailov

Date :   23 Dec 03 (Deposition) - 28 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Uridine Phosphorylase, Nucleoside Phosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. V. Dontsova, A. G. Gabdoulkhakov, A. V. Lyashenko, S. V. Nikonov, S. E. Ealick, A. M. Mikhailov
Structure-Functions Studies Of Uridine Phosphorylase From Salmonella Typhimurium
To Be Published
PubMed: search

Molecule 1 - URIDINE PHOSPHORYLASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	2.4.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PBLUESCRIPT IISK
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	UDP
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	99287
	Strain	:	LT2
	Synonym	:	URDPASE, UPASE

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C	D	E	F
Biological Unit 2 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)	F (1x)
Biological Unit 3 (1x)	:		B				F
Biological Unit 4 (1x)	:			C		E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ACY	-1	Ligand/Ion	ACETIC ACID

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	ACY	-1	Ligand/Ion	ACETIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:26 , ARG B:30 , ARG B:91 , ILE B:92 , GLY B:93 , THR B:94 , GLU B:198 , ARG D:48	BINDING SITE FOR RESIDUE ACY B 254
2	AC2	SOFTWARE	THR B:94 , PHE B:162 , HIS D:8 , ARG D:48	BINDING SITE FOR RESIDUE ACY B 255

(no "SS Bond" information available for 1RYZ)

(no "Cis Peptide Bond" information available for 1RYZ)

(no "SAP(SNP)/Variant" information available for 1RYZ)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	UDP_SALTY	66-81	6	A:66-81 B:66-81 C:66-81 D:66-81 E:66-81 F:66-81

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	UDP_SALTY	66-81	6	A:66-81 B:66-81 C:66-81 D:66-81 E:66-81 F:66-81

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	UDP_SALTY	66-81	6	A:66-81 B:66-81 C:66-81 D:66-81 E:66-81 F:66-81

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	UDP_SALTY	66-81	2	- B:66-81 - - - F:66-81

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNP_UDP_1	PS01232	Purine and other phosphorylases family 1 signature.	UDP_SALTY	66-81	2	- - C:66-81 - E:66-81 -

(no "Exon" information available for 1RYZ)

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:250
 aligned with UDP_SALTY | P0A1F6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:250
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
            UDP_SALTY     4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1ryza_ A: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ryzA00 A:4-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eee...hhhhhhhhhh..eeeee........eeeeee..eeeeee....hhhhhhhhhhhhhhhh..eee.eeeeee.........eeeeeeeeee..hhhhh..........hhhhhhhhhhhhhh...eeeeeeeee.................hhhhhhhhhhhhhhh......hhhhhhhhhh....ee..eeeeeee...........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryz A   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with UDP_SALTY | P0A1F6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:250
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
            UDP_SALTY     4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1ryzb_ B: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ryzB00 B:4-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee..hhhhhhhhhhhh...ee.........eeeee..eee.......hhhhhhhhhhhhhhhhh...ee..eeee.......eeeeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhh....eeeeeeeee.................hhhhhhhhhhhhhh...eee.hhhhhhhhhhh.....eeeeeeeee............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryz B   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain C from PDB  Type:PROTEIN  Length:250
 aligned with UDP_SALTY | P0A1F6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:250
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
            UDP_SALTY     4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1ryzc_ C: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ryzC00 C:4-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh............hhhhhhh...eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhhh.....eeeeeee.........eeeeeeeeee..hhhhh......ee.hhhhhhhhhhhhhhhh..eeeeeeeee.................hhhhhhhhhhhh.....eee.hhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryz C   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain D from PDB  Type:PROTEIN  Length:250
 aligned with UDP_SALTY | P0A1F6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:250
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
            UDP_SALTY     4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1ryzd_ D: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ryzD00 D:4-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh....eee...hhhhhhhhhh.....eeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhh....eeeeeeeee..........eeeeeeee....................hhhhhhhhhhhhhh....eeeee....hhhhh..........hhhhh.hhhhhhh........hhhhhhhhhhh...eeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryz D   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain E from PDB  Type:PROTEIN  Length:250
 aligned with UDP_SALTY | P0A1F6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:250
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
            UDP_SALTY     4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1ryze_ E: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ryzE00 E:4-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh....ee...hhhhhhhhhhh.................eee..eeeee.....hhhhhhhhhhhhhh....eee....ee..........eeeeeeee...hhhhhh......ee..hhhhhhhhhhhhh....eeeeeeee........................hhhhhh...eeeee.hhhhhhhhhhh...eee....eee........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryz E   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain F from PDB  Type:PROTEIN  Length:250
 aligned with UDP_SALTY | P0A1F6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:250
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
            UDP_SALTY     4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1ryzf_ F: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ryzF00 F:4-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ----------------PNP_UDP_1-1ryzF01 F:20-253                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ----------------PNP_UDP_1-1ryzF02 F:20-253                                                                                                                                                                                                                 Pfam domains (2)
           Pfam domains (3) ----------------PNP_UDP_1-1ryzF03 F:20-253                                                                                                                                                                                                                 Pfam domains (3)
           Pfam domains (4) ----------------PNP_UDP_1-1ryzF04 F:20-253                                                                                                                                                                                                                 Pfam domains (4)
           Pfam domains (5) ----------------PNP_UDP_1-1ryzF05 F:20-253                                                                                                                                                                                                                 Pfam domains (5)
           Pfam domains (6) ----------------PNP_UDP_1-1ryzF06 F:20-253                                                                                                                                                                                                                 Pfam domains (6)
         Sec.struct. author .........hhhhh...eee...hhhhhhhhhh.....eeeee....eeeeeee..eeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee.......................hhhhhhhh.eeeee.hhhhhhhhhhh......eeeeeee..........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ryz F   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Phosphorylase/hydrolase-like (558)

Superfamily: Purine and uridine phosphorylases (283)

Family: Purine and uridine phosphorylases (224)

Protein domain: Uridine phosphorylase (42)

Salmonella typhimurium [TaxId: 90371] (23)

1a	d1ryza_	A:
1b	d1ryzb_	B:
1c	d1ryzc_	C:
1d	d1ryzd_	D:
1e	d1ryze_	E:
1f	d1ryzf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1580, no name defined] (194)

Salmonella typhimurium lt2. Organism_taxid: 99287. Strain: lt2. (16)

1a	1ryzA00	A:4-253
1b	1ryzB00	B:4-253
1c	1ryzC00	C:4-253
1d	1ryzD00	D:4-253
1e	1ryzE00	E:4-253
1f	1ryzF00	F:4-253

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PUP (121)

Family: PNP_UDP_1 (121)

Salmonella typhimurium (11)

1a	PNP_UDP_1-1ryzF01	F:20-253
1b	PNP_UDP_1-1ryzF02	F:20-253
1c	PNP_UDP_1-1ryzF03	F:20-253
1d	PNP_UDP_1-1ryzF04	F:20-253
1e	PNP_UDP_1-1ryzF05	F:20-253
1f	PNP_UDP_1-1ryzF06	F:20-253

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (UDP_SALTY | P0A1F6)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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).
	GO:0004850	uridine phosphorylase activity	Catalysis of the reaction: uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.
biological process
	GO:0044206	UMP salvage	Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
	GO:0009116	nucleoside metabolic process	The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
	GO:0009166	nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ryz)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

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	1ryz
		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
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	UDP_SALTY \| P0A1F6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.4.2.3
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	UDP_SALTY \| P0A1F6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (1, 6)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File