4LR8 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   PHOSPHOPENTOMUTASE S154A VARIANT SOAKED WITH RIBOSE 5-PHOSPHATE

Authors :   W. A. Birmingham, C. A. Starbird, T. D. Panosian, D. P. Nannemann, T. M. I B. O. Bachmann

Date :   19 Jul 13 (Deposition) - 31 Jul 13 (Release) - 30 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Alkaline Phosphatase Family, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. R. Birmingham, C. A. Starbird, T. D. Panosian, D. P. Nannemann, T. M. Iverson, B. O. Bachmann
Bioretrosynthetic Construction Of A Didanosine Biosynthetic Pathway.
Nat. Chem. Biol. V. 10 392 2014
PubMed-ID: 24657930 | Reference-DOI: 10.1038/NCHEMBIO.1494

Molecule 1 - PHOSPHOPENTOMUTASE
	Chains	:	A, B, C
	EC Number	:	5.4.2.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BC_4087, DEOB
	Mutation	:	YES
	Organism Scientific	:	BACILLUS CEREUS
	Organism Taxid	:	1396
	Synonym	:	PHOSPHODEOXYRIBOMUTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 17)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HSX	2	Ligand/Ion	5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
3	MN	9	Ligand/Ion	MANGANESE (II) ION
4	TPO	3	Mod. Amino Acid	PHOSPHOTHREONINE
5	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HSX	2	Ligand/Ion	5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
5	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	HSX	-1	Ligand/Ion	5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
5	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	HSX	-1	Ligand/Ion	5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
5	TRS	-1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TPO A:85 , ASP A:156 , ASP A:286 , HIS A:291 , HIS A:339 , HSX A:407	BINDING SITE FOR RESIDUE MN A 401
02	AC2	SOFTWARE	ASP A:13 , TPO A:85 , ASP A:327 , HIS A:328 , HSX A:407	BINDING SITE FOR RESIDUE MN A 402
03	AC3	SOFTWARE	GLY A:27 , ASP A:28 , HIS A:334 , HOH A:634 , HOH A:674 , HOH A:741	BINDING SITE FOR RESIDUE MN A 403
04	AC4	SOFTWARE	TYR A:96 , HOH A:535	BINDING SITE FOR RESIDUE TRS A 404
05	AC5	SOFTWARE	PRO A:351 , LYS A:354 , HOH A:586	BINDING SITE FOR RESIDUE ACT A 405
06	AC6	SOFTWARE	SER A:131 , GLY A:132 , TYR A:152 , ALA A:154 , ASP A:156 , GLN A:160 , ARG A:193 , ARG A:197 , ARG A:208 , HSX A:407 , HOH A:592 , HOH A:621 , HOH A:643 , HOH A:694	BINDING SITE FOR RESIDUE HSX A 406
07	AC7	SOFTWARE	TPO A:85 , ASP A:156 , ARG A:193 , VAL A:283 , ASP A:286 , ALA A:287 , HIS A:291 , HIS A:339 , MN A:401 , MN A:402 , HSX A:406 , HOH A:678 , HOH A:694 , HOH A:752 , HOH A:772	BINDING SITE FOR RESIDUE HSX A 407
08	AC8	SOFTWARE	TPO B:85 , ASP B:156 , ASP B:286 , HIS B:291 , HIS B:339	BINDING SITE FOR RESIDUE MN B 401
09	AC9	SOFTWARE	ASP B:13 , TPO B:85 , ASP B:327 , HIS B:328	BINDING SITE FOR RESIDUE MN B 402
10	BC1	SOFTWARE	ASP B:186 , HOH B:818 , HOH B:819 , HOH B:820	BINDING SITE FOR RESIDUE MN B 403
11	BC2	SOFTWARE	ASP B:264 , HOH B:574 , HOH B:584	BINDING SITE FOR RESIDUE TRS B 404
12	BC3	SOFTWARE	TPO C:85 , ASP C:156 , ASP C:286 , HIS C:291 , HIS C:339	BINDING SITE FOR RESIDUE MN C 401
13	BC4	SOFTWARE	ASP C:13 , TPO C:85 , ASP C:327 , HIS C:328	BINDING SITE FOR RESIDUE MN C 402
14	BC5	SOFTWARE	GLY C:27 , ASP C:28 , HIS C:334 , HOH C:528 , HOH C:554 , HOH C:564	BINDING SITE FOR RESIDUE MN C 403

(no "SS Bond" information available for 4LR8)

(no "Cis Peptide Bond" information available for 4LR8)

(no "SAP(SNP)/Variant" information available for 4LR8)

(no "PROSITE Motif" information available for 4LR8)

(no "Exon" information available for 4LR8)

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:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....ee..hhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeee..eeee....eeee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhh....eeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee................eeeeeeee................hhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lr8 A   2 NKYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTAADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    11        21        31        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 
                                                                                                              85-TPO

Chain B from PDB  Type:PROTEIN  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.........hhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeee..eeee.....eee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhhh...eeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lr8 B   3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTAADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    12        22        32        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
                                                                                                             85-TPO

Chain C from PDB  Type:PROTEIN  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.........hhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhh........eeeeeeeeee..eeee.....eee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhh....eeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lr8 C   3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTAADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    12        22        32        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
                                                                                                             85-TPO

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4LR8)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 17)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (14, 14)

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