4YIK - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'(3')-DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH THE INHIBITOR PB-PVU

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

Date :   20 Nov 13 (Deposition) - 09 Sep 15 (Release) - 09 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.48

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   5'-Nucleotidase, Dephosphorylation, Phosphorylation, Had-Like, Mitochondria, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Pachl, O. Simak, P. Rezacova, M. Fabry, M. Budesinsky, I. Rosenberg J. Brynda
Inhibition Of Human Mitochondrial And Cytosolic 5'(3')-Nucleotidases By Nucleoside Bisphosphonic Acid
Medchemcomm 2015
PubMed: search | Reference-DOI: 10.1039/C5MD00235D

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 13)

Asymmetric Unit (6, 13)

No.	Name	Count	Type	Full Name
1	2O2	1	Ligand/Ion	1-{2-DEOXY-3,5-O-[PHENYL(PHOSPHONO)METHYLIDENE]-BETA-D-THREO-PENTOFURANOSYL}-5-[(E)-2-PHOSPHONOETHENYL]PYRIMIDINE-2,4(1H,3H)-DIONE
2	GOL	4	Ligand/Ion	GLYCEROL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	PEG	5	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PO4	1	Ligand/Ion	PHOSPHATE ION
6	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (5, 24)

No.	Name	Count	Type	Full Name
1	2O2	2	Ligand/Ion	1-{2-DEOXY-3,5-O-[PHENYL(PHOSPHONO)METHYLIDENE]-BETA-D-THREO-PENTOFURANOSYL}-5-[(E)-2-PHOSPHONOETHENYL]PYRIMIDINE-2,4(1H,3H)-DIONE
2	GOL	8	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PEG	10	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PO4	2	Ligand/Ion	PHOSPHATE ION
6	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:41 , ASP A:43 , ASP A:176 , 2O2 A:306 , HOH A:522 , HOH A:528	binding site for residue MG A 301
02	AC2	SOFTWARE	SER A:27 , ASN A:28 , ALA A:119 , THR A:124 , ASP A:125 , VAL A:126 , GLN A:158 , HOH A:470 , HOH A:621	binding site for residue GOL A 302
03	AC3	SOFTWARE	GLY A:110 , GLU A:113 , ALA A:114 , TRP A:214 , ALA A:215 , ASP A:216 , TRP A:218 , HOH A:486 , HOH A:595	binding site for residue GOL A 303
04	AC4	SOFTWARE	TRP A:76 , ARG A:177 , PRO A:178 , ASP A:179 , HOH A:607 , HOH A:613	binding site for residue GOL A 304
05	AC5	SOFTWARE	ARG A:37 , SER A:169 , ALA A:170 , ASP A:171 , SER A:188 , HOH A:416 , HOH A:474 , HOH A:662	binding site for residue GOL A 305
06	AC6	SOFTWARE	ASP A:41 , ASP A:43 , PHE A:49 , PHE A:75 , TRP A:76 , VAL A:77 , TRP A:96 , SER A:131 , ILE A:133 , LYS A:134 , ARG A:163 , MG A:301 , TRS A:307 , HOH A:465 , HOH A:522 , HOH A:523 , HOH A:528 , HOH A:550 , HOH A:575 , HOH A:608 , HOH A:609 , HOH A:610 , HOH A:611 , HOH A:631	binding site for residue 2O2 A 306
07	AC7	SOFTWARE	ASP A:43 , PHE A:49 , PHE A:102 , ILE A:133 , 2O2 A:306 , HOH A:550	binding site for residue TRS A 307
08	AC8	SOFTWARE	ARG A:72 , ARG A:73 , CYS A:197 , HIS A:198 , ASN A:199 , GLN A:200 , HIS A:201 , LEU A:202 , HOH A:572 , HOH A:645	binding site for residue PEG A 308
09	AC9	SOFTWARE	GLU A:148 , ARG A:210 , HIS A:212 , ASP A:216 , HOH A:404 , HOH A:405 , HOH A:421 , HOH A:423 , HOH A:430	binding site for residue PEG A 309
10	AD1	SOFTWARE	ASN A:28 , ALA A:29 , GLY A:33 , ARG A:34 , ALA A:35 , ASP A:125 , ALA A:183 , HOH A:435 , HOH A:476	binding site for residue PEG A 310
11	AD2	SOFTWARE	PHE A:103 , LYS A:149 , PRO A:207 , ARG A:208 , ARG A:209 , HOH A:420 , HOH A:452	binding site for residue PEG A 311
12	AD3	SOFTWARE	GLU A:104 , LYS A:149 , HOH A:413 , HOH A:513 , HOH A:654 , HOH A:659	binding site for residue PEG A 312
13	AD4	SOFTWARE	PRO A:178 , ASP A:179 , ILE A:180 , TRP A:189 , HIS A:191 , ARG A:208 , HOH A:588	binding site for residue PO4 A 313

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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)
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Chain A from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.eee..........eeee..............eeeee..............eee.....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yik A  27 SNAASGGRALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP 227
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226

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Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (14, 14)

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