1T8Q - JenaLib

Asym.Unit - manually (Jmol Viewer)

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)

Title :   STRUCTURAL GENOMICS, CRYSTAL STRUCTURE OF GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE FROM E. COLI

Authors :   R. Zhang, Y. Kim, I. Dementieva, N. Duke, L. Stols, M. Donnelly, A. Joach Midwest Center For Structural Genomics (Mcsg)

Date :   13 May 04 (Deposition) - 03 Aug 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Phosphodiesterase, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Zhang, Y. Kim, I. Dementieva, N. Duke, L. Stols, M. Donnelly, A. Joachimiak
The Crystal Structure Of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
To Be Published
PubMed: search

Molecule 1 - GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE, PERIPLASMIC
	Chains	:	A, B, C, D
	EC Number	:	3.1.4.46
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PDM68
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	GLPQ, B2239
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 51)

No.	Name	Count	Type	Full Name
1	GOL	11	Ligand/Ion	GLYCEROL
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	MSE	36	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 24)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 23)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:63 , ASP A:65 , GLU A:171 , GOL A:1605 , HOH A:1615	BINDING SITE FOR RESIDUE MG A 1601
02	AC2	SOFTWARE	GLU B:63 , ASP B:65 , GLU B:171 , GOL B:1606 , HOH B:1612	BINDING SITE FOR RESIDUE MG B 1602
03	AC3	SOFTWARE	GLU C:63 , ASP C:65 , GLU C:171 , GOL C:1607 , HOH C:1614	BINDING SITE FOR RESIDUE MG C 1603
04	AC4	SOFTWARE	GLU D:63 , ASP D:65 , GLU D:171 , GOL D:1608 , HOH D:1616	BINDING SITE FOR RESIDUE MG D 1604
05	AC5	SOFTWARE	HIS A:36 , ARG A:37 , GLU A:63 , ASP A:65 , GLU A:171 , LYS A:173 , TYR A:313 , MG A:1601 , HOH A:1615 , HOH A:1616 , HOH A:1657 , HOH A:1905	BINDING SITE FOR RESIDUE GOL A 1605
06	AC6	SOFTWARE	HIS B:36 , ARG B:37 , GLU B:63 , ASP B:65 , GLU B:171 , LYS B:173 , PHE B:210 , MG B:1602 , HOH B:1612 , HOH B:1613 , HOH B:1677	BINDING SITE FOR RESIDUE GOL B 1606
07	AC7	SOFTWARE	HIS C:36 , ARG C:37 , GLU C:63 , GLU C:171 , LYS C:173 , PHE C:210 , TYR C:313 , MG C:1603 , HOH C:1653 , HOH C:1739	BINDING SITE FOR RESIDUE GOL C 1607
08	AC8	SOFTWARE	HIS D:36 , ARG D:37 , GLU D:63 , ASP D:65 , GLU D:171 , LYS D:173 , PHE D:210 , MG D:1604 , HOH D:1616 , HOH D:1639 , HOH D:1746	BINDING SITE FOR RESIDUE GOL D 1608
09	AC9	SOFTWARE	LYS A:195 , HOH A:1811 , HOH A:1955 , HOH A:1962	BINDING SITE FOR RESIDUE GOL A 1609
10	BC1	SOFTWARE	LYS B:195 , HOH B:1847 , HOH B:1870	BINDING SITE FOR RESIDUE GOL B 1610
11	BC2	SOFTWARE	LYS B:140 , LYS C:195 , TYR C:196 , HOH C:1750	BINDING SITE FOR RESIDUE GOL C 1611
12	BC3	SOFTWARE	LYS D:195 , TYR D:196	BINDING SITE FOR RESIDUE GOL D 1612
13	BC4	SOFTWARE	ARG C:95 , ALA C:96 , ASP C:106 , HOH C:1862	BINDING SITE FOR RESIDUE GOL C 1613
14	BC5	SOFTWARE	ARG A:95 , ASP A:106 , HOH A:1779 , HOH A:1909 , HOH A:1910	BINDING SITE FOR RESIDUE GOL A 1614
15	BC6	SOFTWARE	ARG D:95 , ARG D:97 , ASP D:106 , HOH D:1728 , HOH D:1736	BINDING SITE FOR RESIDUE GOL D 1615

(no "SS Bond" information available for 1T8Q)

Asymmetric Unit

No.	Residues
1	Tyr A:313	-	Thr A:314
2	Tyr B:313	-	Thr B:314
3	Tyr C:313	-	Thr C:314
4	Tyr D:313	-	Thr D:314

(no "SAP(SNP)/Variant" information available for 1T8Q)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GP_PDE	PS51704	GP-PDE domain profile.	GLPQ_ECOLI	31-355	4	A:31-355 B:31-355 C:31-355 D:31-355

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GP_PDE	PS51704	GP-PDE domain profile.	GLPQ_ECOLI	31-355	2	A:31-355 - - D:31-355

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GP_PDE	PS51704	GP-PDE domain profile.	GLPQ_ECOLI	31-355	2	- B:31-355 C:31-355 -

(no "Exon" information available for 1T8Q)

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:328
 aligned with GLPQ_ECOLI | P09394 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:328
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348        
           GLPQ_ECOLI    29 NEKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
               SCOP domains d1t8qa_ A: Glycerophosphodiester phosphodiesterase GlpQ                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1t8qA00 A:29-356 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhh...eeeeeeee.....eee..........hhhhhh..........hhhhhhhhhhhh......eeee..eeee................hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh..hhhhhhhhhhhhh.........eeee.hhhhhhhhhhh.hhhhh...eeeeee.hhhhh..eee.....eee..hhhhhh..hhhhhhh...eeee.hhhh.............hhhhhhhhh..ee...............hhhhhhhhhhh.....eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GP_PDE  PDB: A:31-355 UniProt: 31-355                                                                                                                                                                                                                                                                                                - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t8q A  29 NEKIVIAHRGASGYLPEHTLPAKAmAYAQGADYLEQDLVmTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPmGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKmGmELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWmFKPGAmKQVAEYADGIGPDYHmLIEETSQPGNIKLTGmVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
                                    38        48    |   58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  |    268       278    |  288       298|      308       318       328       338       348        
                                                   53-MSE         68-MSE                                                               138-MSE                                                                                 226-MSE                            261-MSE |             283-MSE         299-MSE                                                     
                                                                                                                                                                                                                                 228-MSE                                267-MSE

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with GLPQ_ECOLI | P09394 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:329
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348         
           GLPQ_ECOLI    29 NEKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLNK 357
               SCOP domains d1t8qb_ B: Glycerophosphodiester phosphodiesterase GlpQ                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1t8qB00 B:29-357 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhh..eeeeeeee.....eee..........hhhhhh..........hhhhhhhhhhhh......eeee..eeee................hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh..hhhhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhh....eeeeee.hhhhh..eee.....eee..hhhhhh.hhhhhhh....eeee.hhhh.............hhhhhhhhh..ee...............hhhhhhhhhhh.....eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GP_PDE  PDB: B:31-355 UniProt: 31-355                                                                                                                                                                                                                                                                                                -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t8q B  29 NEKIVIAHRGASGYLPEHTLPAKAmAYAQGADYLEQDLVmTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPmGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKmGmELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWmFKPGAmKQVAEYADGIGPDYHmLIEETSQPGNIKLTGmVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLNK 357
                                    38        48    |   58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  |    268       278    |  288       298|      308       318       328       338       348         
                                                   53-MSE         68-MSE                                                               138-MSE                                                                                 226-MSE                            261-MSE |             283-MSE         299-MSE                                                      
                                                                                                                                                                                                                                 228-MSE                                267-MSE

Chain C from PDB  Type:PROTEIN  Length:328
 aligned with GLPQ_ECOLI | P09394 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:328
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348        
           GLPQ_ECOLI    29 NEKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
               SCOP domains d1t8qc_ C: Glycerophosphodiester phosphodiesterase GlpQ                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1t8qC00 C:29-356 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhh...eeeeeeee.....eee..........hhhhhh..........hhhhhhhhhhh.......eeee..eeee................hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh..hhhhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhhh...eeeeee.hhhhh..eee.....eee..hhhhhh.hhhhhhh....eeee.hhhh.............hhhhhhhh...ee...............hhhhhhhhhhh.....eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GP_PDE  PDB: C:31-355 UniProt: 31-355                                                                                                                                                                                                                                                                                                - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t8q C  29 NEKIVIAHRGASGYLPEHTLPAKAmAYAQGADYLEQDLVmTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPmGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKmGmELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWmFKPGAmKQVAEYADGIGPDYHmLIEETSQPGNIKLTGmVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
                                    38        48    |   58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  |    268       278    |  288       298|      308       318       328       338       348        
                                                   53-MSE         68-MSE                                                               138-MSE                                                                                 226-MSE                            261-MSE |             283-MSE         299-MSE                                                     
                                                                                                                                                                                                                                 228-MSE                                267-MSE

Chain D from PDB  Type:PROTEIN  Length:327
 aligned with GLPQ_ECOLI | P09394 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:327
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       
           GLPQ_ECOLI    30 EKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
               SCOP domains d1t8qd_ D: Glycerophosphodiester phosphodiesterase GlpQ                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1t8qD00 D:30-356 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) ------GDPD-1t8qD01 D:36-350                                                                                                                                                                                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) ------GDPD-1t8qD02 D:36-350                                                                                                                                                                                                                                                                                                      ------ Pfam domains (2)
           Pfam domains (3) ------GDPD-1t8qD03 D:36-350                                                                                                                                                                                                                                                                                                      ------ Pfam domains (3)
           Pfam domains (4) ------GDPD-1t8qD04 D:36-350                                                                                                                                                                                                                                                                                                      ------ Pfam domains (4)
         Sec.struct. author ..eeee...........hhhhhhhhhhh...eeeeeeee.....eee..........hhhhhh..........hhhhhhhhhhhh......eeee..eeee................hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh..hhhhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhhh...eeeeee.hhhhh..eee.....eee..hhhhhh..hhhhhh....eeee.hhhhh............hhhhhhhhh..ee...............hhhhhhhhhhh.....eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GP_PDE  PDB: D:31-355 UniProt: 31-355                                                                                                                                                                                                                                                                                                - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t8q D  30 EKIVIAHRGASGYLPEHTLPAKAmAYAQGADYLEQDLVmTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGKKVQTYPGRFPmGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKmGmELNLVQLIAYTDWNETQQKQPDGSWVNYNYDWmFKPGAmKQVAEYADGIGPDYHmLIEETSQPGNIKLTGmVQDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLN 356
                                    39        49   |    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      |229       239       249       259 |     269       279   |   289       299       309       319       329       339       349       
                                                  53-MSE         68-MSE                                                               138-MSE                                                                                 226-MSE                            261-MSE |             283-MSE         299-MSE                                                     
                                                                                                                                                                                                                                228-MSE                                267-MSE

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: TIM beta/alpha-barrel (3956)

Superfamily: PLC-like phosphodiesterases (46)

Family: Glycerophosphoryl diester phosphodiesterase (7)

Protein domain: Glycerophosphodiester phosphodiesterase GlpQ (2)

Escherichia coli [TaxId: 562] (2)

1a	d1t8qa_	A:
1b	d1t8qb_	B:
1c	d1t8qc_	C:
1d	d1t8qd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Phosphatidylinositol (PI) phosphodiesterase (37)

Escherichia coli. Organism_taxid: 562. (2)

1a	1t8qD00	D:30-356
1b	1t8qA00	A:29-356
1c	1t8qC00	C:29-356
1d	1t8qB00	B:29-357

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLC (20)

Family: GDPD (8)

Escherichia coli (strain K12) (2)

1a	GDPD-1t8qD01	D:36-350
1b	GDPD-1t8qD02	D:36-350
1c	GDPD-1t8qD03	D:36-350
1d	GDPD-1t8qD04	D:36-350

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GLPQ_ECOLI | P09394)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0008889	glycerophosphodiester phosphodiesterase activity	Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
	GO:0006071	glycerol metabolic process	The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	Cis Peptide Bonds
		Tyr A:313 - Thr A:314	[ RasMol ]
		Tyr B:313 - Thr B:314	[ RasMol ]
		Tyr C:313 - Thr C:314	[ RasMol ]
		Tyr D:313 - Thr D:314	[ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1t8q
		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
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	GLPQ_ECOLI \| P09394
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	3.1.4.46
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	GLPQ_ECOLI \| P09394
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GLPQ_ECOLI \| P09394	:	1ydy

(no "Related Entries Specified in the PDB File" available for 1T8Q)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 51)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (8, 8)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File