Structure of PDB 3vth Chain B Binding Site BS03

Receptor Information
>3vth Chain B (length=630) Species: 273068 (Caldanaerobacter subterraneus subsp. tengcongensis MB4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFVPVSPDMGVCEDCLRELKDPKDRRYRYPFINCTNCGPRFSIIEDIPYD
RAKTSMKVFPSREYHDPHDRRFHAQPVAEIKCVAKALKEGKIVAIKGIGG
FHLAVNALDDEAVATLRRRKKRYGKPFAVMMRDVEEVKKYCIVSPEEERL
LLSQRRPIVLLKKKGEKLAKGIADDLDTLGVMLPYAPIHYLLMEEIDFPI
VMTSGNVSEEPICKDNEEALEKLKDIADVFLLNNRDIVNRIDDSVTSFNA
GAERIIRRARGYAPQPILLKKEVKASILAVGGFYKNTFCMTKGHYAFISH
HIGDLDNEKAFNYYIEQIERYKKLFRVDPEVVAHDMHKGYLSTQYAKSLD
LPKIEVQHHHAHIASCMAEHNLDEKVIGIAYDGTGYGTDGNVWGAEILVC
DLKSFERIAHLKYKPLPGNELAIKKIYRTALGFIFDNISFYKNFVEQVDS
RELDIILKQIDRKINTAYVSSMGRFFDAVAALIGVRKEVLFEGQAAMELE
SLMAESEEYYEYEILKEDRYVIDPELILRQIYEDYMKGFEKSYISAKFHN
TVVNFTYDLANLIRKETGINKVVLSGGSFQNRYLLRRLIEKLSLSGFEVY
SNSKVPCNDGGISLGQAVIANKILEGSAWS
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain3vth Chain B Residue 804 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3vth Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases
Resolution2.0 Å
Binding residue
(original residue number in PDB)		K245 R247 K250 P251 L285 T303 L304 T328 S329 S333 E334 R382
Binding residue
(residue number reindexed from 1)		K120 R122 K125 P126 L160 T178 L179 T203 S204 S208 E209 R257
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.1.7: acylphosphatase.
6.2.-.-
Gene Ontology
Molecular Function
GO:0003725 double-stranded RNA binding
GO:0003998 acylphosphatase activity
GO:0008270 zinc ion binding
GO:0016743 carboxyl- or carbamoyltransferase activity
GO:0016787 hydrolase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0046944 protein carbamoylation
GO:0051604 protein maturation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vth, PDBe:3vth, PDBj:3vth
PDBsum3vth
PubMed22740694
UniProtQ8RDB0

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