Structure of PDB 6a4d Chain B Binding Site BS03

Receptor Information
>6a4d Chain B (length=182) Species: 167879 (Colwellia psychrerythraea 34H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMAGNDSNLIWLDLEMTGLEPVEDVILEIAIIITDSELNILAQGPIFAIS
QTDDVLDNMNPWCIEHHGKSGLTQRCRDSEVSLAHATKESLAFVQEWVPQ
GKSPMCGNSIGQDRRFINKYMPDFEDHFHYRNLDVSTIKELAKRWKPEVL
ESVVKTGAHLALDAIKESIAELKVYRELFFKL
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)		N107 S108 Q111 S135 K138 E166 E170
Binding residue
(residue number reindexed from 1)		N108 S109 Q112 S136 K139 E167 E171
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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