4L57 - JenaLib

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Title :   HIGH RESOLUTIN STRUCTURE OF HUMAN CYTOSOLIC 5'(3')-DEOXYRIBONUCLEOTIDASE

Authors :   P. Pachl, J. Brynda, P. Rezacova

Date :   10 Jun 13 (Deposition) - 12 Feb 14 (Release) - 19 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.08

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

Keywords :   5'-Nucleotidase, Protein Conformation, Sequence Homology, Had-Like, Hydrolase, Dephosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Pachl, M. Fabry, I. Rosenberg, O. Simak, P. Rezacova, J. Brynda
Structures Of Human Cytosolic And Mitochondrial Nucleotidases: Implications For Structure-Based Design Of Selective Inhibitors
Acta Crystallogr. , Sect. D V. 70 461 2014
PubMed: search | Reference-DOI: 10.1107/S139900471303050

Molecule 1 - 5'(3')-DEOXYRIBONUCLEOTIDASE, CYTOSOLIC TYPE
	Chains	:	A, B
	EC Number	:	3.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 22
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-195
	Gene	:	DNT1, NT5C, UMPH2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYTOSOLIC 5',3'-PYRIMIDINE NUCLEOTIDASE, DEOXY-5'- NUCLEOTIDASE 1, DNT-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	NA	1	Ligand/Ion	SODIUM ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:10 , ASP A:12 , ASP A:145 , PO4 A:202 , HOH A:311 , HOH A:320	BINDING SITE FOR RESIDUE MG A 201
02	AC2	SOFTWARE	ASP A:10 , MET A:11 , ASP A:12 , THR A:99 , SER A:100 , LYS A:112 , LYS A:134 , MG A:201 , GOL A:204 , HOH A:301 , HOH A:311 , HOH A:320 , HOH A:535	BINDING SITE FOR RESIDUE PO4 A 202
03	AC3	SOFTWARE	ASN A:186 , ARG A:188 , GLU A:189 , HOH A:335 , HOH A:391 , HOH A:524 , HOH B:336 , HOH B:353	BINDING SITE FOR RESIDUE GOL A 203
04	AC4	SOFTWARE	PHE A:18 , GLU A:19 , PHE A:44 , PO4 A:202 , GOL A:207 , HOH A:320 , HOH A:326 , HOH A:500 , HOH A:510	BINDING SITE FOR RESIDUE GOL A 204
05	AC5	SOFTWARE	PHE A:44 , SER A:100 , ARG A:132 , HOH A:301 , HOH A:389 , HOH A:546	BINDING SITE FOR RESIDUE GOL A 205
06	AC6	SOFTWARE	ARG A:51 , ASP A:59 , GLU A:117 , GLN A:118 , HOH A:318 , HOH A:332 , HOH A:520	BINDING SITE FOR RESIDUE GOL A 206
07	AC7	SOFTWARE	PHE A:18 , PHE A:44 , LEU A:45 , ALA A:46 , ARG A:47 , TYR A:65 , GOL A:204 , HOH A:410 , HOH A:511	BINDING SITE FOR RESIDUE GOL A 207
08	AC8	SOFTWARE	ASN A:88 , LEU A:90 , THR A:93 , HOH A:423 , HOH A:429	BINDING SITE FOR RESIDUE NA A 208
09	AC9	SOFTWARE	ASP B:10 , ASP B:12 , ASP B:145 , PO4 B:202 , HOH B:314 , HOH B:315	BINDING SITE FOR RESIDUE MG B 201
10	BC1	SOFTWARE	ASP B:10 , MET B:11 , ASP B:12 , THR B:99 , SER B:100 , LYS B:112 , LYS B:134 , MG B:201 , GOL B:203 , HOH B:301 , HOH B:314 , HOH B:315 , HOH B:371	BINDING SITE FOR RESIDUE PO4 B 202
11	BC2	SOFTWARE	ASP B:12 , PHE B:18 , PHE B:44 , LEU B:45 , PHE B:71 , LEU B:102 , PO4 B:202 , HOH B:371 , HOH B:384 , HOH B:479	BINDING SITE FOR RESIDUE GOL B 203

(no "SS Bond" information available for 4L57)

(no "Cis Peptide Bond" information available for 4L57)

(no "SAP(SNP)/Variant" information available for 4L57)

(no "PROSITE Motif" information available for 4L57)

(no "Exon" information available for 4L57)

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4l57a_ A: automated matches                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhhhh.eee..hhhhh...eeee..............eeeee.hhhhh.........ee.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l57 A   4 SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETPSWEHILFTCCHNRHLVLPPTRRRLLSWSDNWREILDSKR 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193

Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4l57b_ B: automated matches                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhhhh.eee..hhhhh...eeee..............eeeee...............ee.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l57 B   4 SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETPSWEHILFTCCHNRHLVLPPTRRRLLSWSDNWREILDSKR 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193

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	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

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

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: 5'(3')-deoxyribonucleotidase (dNT-2) (18)

Protein domain: automated matches (14)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d4l57a_	A:
1b	d4l57b_	B:

(no "CATH Domain" information available for 4L57)

(no "Pfam Domain" information available for 4L57)

Asymmetric Unit(hide GO term definitions)

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		Biological Unit 1	[ Jena3D ]

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	4l57
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Description

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Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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