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4L6C
Asym. Unit
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Asym.Unit (83 KB)
Biol.Unit 1 (152 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH THE INHIBITOR PIB-T
Authors
:
P. Pachl, J. Brynda, P. Rezacova
Date
:
12 Jun 13 (Deposition) - 10 Sep 14 (Release) - 08 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
5'-Nucleotidase, Mitochondria, Protein Conformation, Sequence Homology, Had-Like, Hydrolase, Dephosphorylation, Phosphorylation, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Simak, P. Pachl, M. Fabry, M. Budesinsky, T. Jandusik, A. Hnizda, R. Sklenickova, M. Petrova, V. Veverka, P. Rezacova, J. Brynda, I. Rosenberg
Conformationally Constrained Nucleoside Phosphonic Acids - Potent Inhibitors Of Human Mitochondrial And Cytosolic 5'(3')-Nucleotidases.
Org. Biomol. Chem. V. 12 7971 2014
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Hetero Components
(5, 12)
Info
All Hetero Components
1a: 1-{2-DEOXY-3,5-O-[(4-IODOPHENYL)(P... (0BTa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
4a: MAGNESIUM ION (MGa)
5a: PHOSPHATE ION (PO4a)
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No.
Name
Count
Type
Full Name
1
0BT
1
Ligand/Ion
1-{2-DEOXY-3,5-O-[(4-IODOPHENYL)(PHOSPHONO)METHYLIDENE]-BETA-D-THREO-PENTOFURANOSYL}-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
7
Ligand/Ion
GLYCEROL
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
PO4
1
Ligand/Ion
PHOSPHATE ION
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Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:41 , ASP A:43 , ASP A:176 , PO4 A:302 , HOH A:417 , HOH A:418
BINDING SITE FOR RESIDUE MG A 301
02
AC2
SOFTWARE
ASP A:41 , MET A:42 , ASP A:43 , THR A:130 , SER A:131 , LYS A:165 , MG A:301 , 0BT A:303 , HOH A:417 , HOH A:439
BINDING SITE FOR RESIDUE PO4 A 302
03
AC3
SOFTWARE
PHE A:75 , TRP A:76 , VAL A:77 , TRP A:96 , ILE A:133 , LYS A:134 , ARG A:163 , PO4 A:302 , HOH A:415 , HOH A:418 , HOH A:447 , HOH A:449 , HOH A:567
BINDING SITE FOR RESIDUE 0BT A 303
04
AC4
SOFTWARE
ARG A:73 , GLY A:74 , HIS A:198 , ASN A:199 , GLN A:200 , HIS A:201 , LEU A:202 , HOH A:471 , HOH A:500
BINDING SITE FOR RESIDUE GOL A 304
05
AC5
SOFTWARE
SER A:27 , ASN A:28 , ALA A:119 , THR A:124 , ASP A:125 , VAL A:126 , GLN A:158 , GOL A:309 , HOH A:490
BINDING SITE FOR RESIDUE GOL A 305
06
AC6
SOFTWARE
TRP A:76 , ARG A:177 , PRO A:178 , ASP A:179
BINDING SITE FOR RESIDUE GOL A 306
07
AC7
SOFTWARE
TYR A:138 , TRP A:214 , ALA A:215 , ASP A:216 , ASP A:217 , TRP A:218 , LYS A:219 , HOH A:510
BINDING SITE FOR RESIDUE GOL A 307
08
AC8
SOFTWARE
ASP A:48 , LEU A:108 , ALA A:196 , CYS A:197 , HOH A:436 , HOH A:484 , HOH A:511
BINDING SITE FOR RESIDUE GOL A 308
09
AC9
SOFTWARE
ASP A:154 , GLN A:158 , GOL A:305
BINDING SITE FOR RESIDUE GOL A 309
10
BC1
SOFTWARE
ARG A:37 , SER A:169 , ALA A:170 , ASP A:171 , GLU A:184 , HOH A:470
BINDING SITE FOR RESIDUE GOL A 310
11
BC2
SOFTWARE
PRO A:65 , PHE A:66 , HOH A:448
BINDING SITE FOR RESIDUE EDO A 311
12
BC3
SOFTWARE
ASN A:28 , ALA A:29 , GLY A:33 , ARG A:34 , ALA A:35 , ASP A:125 , ALA A:183 , PRO A:185 , HOH A:538
BINDING SITE FOR RESIDUE EDO A 312
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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SCOP Domains
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CATH Domains
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Pfam Domains
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Chain A
Asymmetric Unit 1
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Asym.Unit (83 KB)
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