Structure of PDB 5a2y Chain B Binding Site BS01

Receptor Information
>5a2y Chain B (length=464) Species: 9031 (Gallus gallus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTFTEVQTERLEQADRSVLIKCPSKLNEKKLLQYLSSHGKIDNYFFFENR
GIHALIEFSEKSSVASLQAVTGIPKHHVVPYKSRLFTFTLKNPGSQAEER
PVKISPQSHIPVNELIPKLCHADSISSQMYILLNEYQLTEENIKLRYLAC
SLVRDFARAYFPDSTVKPFGSSVNTFGKLGCDVDMFLDFHDKKGPFEMEY
QMKRLPSERLATQKILSIIGDCLDNFGPGYSSVQKILNARCPLVKFSHQP
TGFQCDLSVSNSIAIRCSELLYIYGCLDPRVRALVFSLRCWARVHGLTNS
VPGTWITNFSLTMMIMFFLQKRSPPIIPTLDQLKELADEKDKHVIGGYDC
SFVSDLSKIKPTKNTETLDELLCDFFQYFGNFDFRKNSLNLRKGKEVNKP
ESSPLYIWNPFEQDLNISKNVNQPQLEKFVAMARESAWILQKEDKTQQMI
NKEPWGLAAVLIPF
Ligand information
Ligand IDUTP
InChIInChI=1S/C9H15N2O15P3/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPGAVKCOVUIYSFO-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H15 N2 O15 P3
NameURIDINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL336296
DrugBankDB04005
ZINCZINC000003861755
PDB chain5a2y Chain B Residue 1528 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5a2y Structure of Mitochondrial Poly(A) RNA Polymerase Reveals the Structural Basis for Dimerization, ATP Selectivity and the Spax4 Disease Phenotype.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		G225 S226 N371
Binding residue
(residue number reindexed from 1)		G170 S171 N308
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) G283 G290 K298 I408 S465
Catalytic site (residue number reindexed from 1) G220 G227 K235 I345 S402
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0002134 UTP binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016740 transferase activity
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:1990817 poly(A) RNA polymerase activity
Biological Process
GO:0000965 mitochondrial RNA 3'-end processing
GO:0016070 RNA metabolic process
GO:0071044 histone mRNA catabolic process
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5a2y, PDBe:5a2y, PDBj:5a2y
PDBsum5a2y
PubMed26319014
UniProtF1NBW0

[Back to BioLiP]