Structure of PDB 6a4d Chain A Binding Site BS03

Receptor Information
>6a4d Chain A (length=184) Species: 167879 (Colwellia psychrerythraea 34H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMAGNDSNLIWLDLEMTGLEPVEDVILEIAIIITDSELNILAQGPIFA
ISQTDDVLDNMNPWCIEHHGKSGLTQRCRDSEVSLAHATKESLAFVQEWV
PQGKSPMCGNSIGQDRRFINKYMPDFEDHFHYRNLDVSTIKELAKRWKPE
VLESVVKTGAHLALDAIKESIAELKVYRELFFKL
Ligand information
Ligand ID9RC
InChIInChI=1S/C16H18N3O10P/c1-9-7-18(16(22)17-15(9)21)14-6-12(20)13(28-14)8-27-30(25,26)29-11-4-2-10(3-5-11)19(23)24/h2-5,7,12-14,20H,6,8H2,1H3,(H,25,26)(H,17,21,22)/t12-,13+,14+/m0/s1
InChIKeyRWOAVOYBVRQNIZ-BFHYXJOUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)Oc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O
OpenEye OEToolkits 2.0.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)Oc3ccc(cc3)[N+](=O)[O-])O
ACDLabs 12.01O=C1NC(=O)C(C)=CN1C2CC(O)C(O2)COP(Oc3ccc([N+]([O-])=O)cc3)(=O)O
CACTVS 3.385CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)Oc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O
OpenEye OEToolkits 2.0.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)Oc3ccc(cc3)[N+](=O)[O-])O
FormulaC16 H18 N3 O10 P
Name5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine;
PNP-TMP
ChEMBLCHEMBL596169
DrugBank
ZINCZINC000013520531
PDB chain6a4d Chain B Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6a4d Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		Y129 R130
Binding residue
(residue number reindexed from 1)		Y132 R133
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.15.-
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003676 nucleic acid binding
GO:0004527 exonuclease activity
GO:0016896 RNA exonuclease activity, producing 5'-phosphomonoesters
Biological Process
GO:0006259 DNA metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6a4d, PDBe:6a4d, PDBj:6a4d
PDBsum6a4d
PubMed30804410
UniProtQ47VZ4|ORN_COLP3 Oligoribonuclease (Gene Name=orn)

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