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Title :   CRYSTAL STRUCTURE OF E.COLI LIGT COMPLEXED WITH 3'-AMP

Authors :   M. Myllykoski, P. Kursula

Date :   27 Jun 16 (Deposition) - 18 Jan 17 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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 :   Enzyme, 2H Phosphoesterase/Ligase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Myllykoski, P. Kursula
Structural Aspects Of Nucleotide Ligand Binding By A Bacterial 2H Phosphoesterase.
Plos One V. 12 70355 2017
PubMed-ID: 28141848 | Reference-DOI: 10.1371/JOURNAL.PONE.0170355

Compounds

Molecule 1 - RNA 2',3'-CYCLIC PHOSPHODIESTERASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PTH 27
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	THPR, ECBD_3472
	Organism Scientific	:	ESCHERICHIA COLI BL21(DE3)
	Organism Taxid	:	469008
	Synonym	:	RNA 2',3'-CPDASE

Structural Features

Chains, Units

		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)

Ligands, Modified Residues, Ions (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	3AM	1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGEN PHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3AM	1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGEN PHOSPHATE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	3AM	-1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGEN PHOSPHATE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	3AM	-1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGEN PHOSPHATE

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	3AM	-1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGEN PHOSPHATE

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:8 , HIS A:43 , THR A:45 , PHE A:48 , PHE A:116 , HIS A:125 , THR A:127 , ARG A:130 , HOH A:302 , GLU D:19 , HIS D:23	binding site for residue 3AM A 201

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhee.hhhh.eeeeeeeeeehhhhhhhhhhhhhh.....eeee..eeeee....eeeee....hhhhhhhhhhhhhhhhh............eeeeee...............eeee.eeeeeeeee....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ldo A   3 EPQRLFFAIDLPAEIREQIIHWRAKHFPPEAGRPVAADNLHLTLAFLGEVSAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQLANMLRSQAARSGCFQSNRPFHPHITLLRDASEAVTIPPPGFNWSYAVTEFTLYASSFARGRTRYTPLKRWALTQ 176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhee.hhhh.eeeeeeeeeehhhhhhhhhhhhhh.....eeee..eeeee....eeeee....hhhhhhhhhhhhhhhhh........eeeeee...............eeee.eeeeeeeee....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ldo B   3 EPQRLFFAIDLPAEIREQIIHWRAKHFPPEAGRPVAADNLHLTLAFLGEVSAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQLANMLRSQAARSGCFPFHPHITLLRDASEAVTIPPPGFNWSYAVTEFTLYASSFARGRTRYTPLKRWALTQ 176
                                    12        22        32        42        52        62        72        82        92       102       112   ||  126       136       146       156       166       176
                                                                                                                                           116|                                                       
                                                                                                                                            121

Chain C from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhhhhhhhhee.hhhhh.eeeeeeee.hhhhhhhhhhhhhh.....eeee..eeeee....eeeee....hhhhhhhhhhhhhhhhh....eeeeee...............eeee.eeeeeeeeee..eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ldo C   3 EPQRLFFAIDLPAEIREQIIHWRAKHFPPEAGRPVAADNLHLTLAFLGEVSAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQLANMLRSQAARPFHPHITLLRDASEAVTIPPPGFNWSYAVTEFTLYASSFARGRTRYTPLKRWALTQ 176
                                    12        22        32        42        52        62        72        82        92       102       112|      130       140       150       160       170      
                                                                                                                                       112|                                                       
                                                                                                                                        121

Chain D from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhhhhhhhhhee.hhhhh.eeeeeeeeehhhhhhhhhhhhhh.....eeee..eeeee....eeeee....hhhhhhhhhhhhhhhhh.....eeeeee...............eeee.eeeeeeeee....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ldo D   2 SEPQRLFFAIDLPAEIREQIIHWRAKHFPPEAGRPVAADNLHLTLAFLGEVSAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQLANMLRSQAARSGFHPHITLLRDASEAVTIPPPGFNWSYAVTEFTLYASSFARGRTRYTPLKRWALTQ 176
                                    11        21        31        41        51        61        71        81        91       101       111  ||   128       138       148       158       168        
                                                                                                                                          114|                                                      
                                                                                                                                           122

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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Description