Structure of PDB 6chs Chain D Binding Site BS02

Receptor Information
>6chs Chain D (length=550) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NEVGYDDIGGCRKQLAQIREMVELPLRHPQLFKSIGIKPPRGVLLYGPPG
TGKTLMARAVANETGAFFFLINGPEIMSKMAGESESNLRKAFEEAEKNSP
AIIFIDEIDSIAPKREKTNGEVERRVVSQLLTLMDGMKARSNVVVMAATN
RPNSIDPALRRFGRFDREVDIGIPDPTGRLEILQIHTKNMKLADDVDLEQ
IAAETHGYVGSDLAALCSEAAMQQIREKMDLIDLDEDTIDAEVLDSLGVT
MDNFRYALGVSNPSALREVAVVEVPNVRWEDIGGLEQVKQELKEQVQYPV
DHPEKFLKFGLSPSRGVLFYGPPGTGKTMLAKAVANECAANFISVKGPEL
LSMWFGESESNIRDIFDKARAAAPCVVFLDELDSIAKARGGSIGDAGGAS
DRVVNQLLTEMDGMTSKKNVFVIGATNRPEQLDPALCRPGRLDQLIYVPL
PDEAGRLSILKAQLRKTPVSKDVDLAYIASKTHGFSGADLAFITQRAVKL
AIKESIAAEIEPVPELTKRHFEEAMRDARRSVSDVEIRRYEAFAQQMKNA
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain6chs Chain D Residue 902 [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]
PDB6chs Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Resolution4.3 Å
Binding residue
(original residue number in PDB)		P537 G538 T539 G540 K541 T542 M543 I673 Q677 G701 A702
Binding residue
(residue number reindexed from 1)		P323 G324 T325 G326 K327 T328 M329 I459 Q463 G487 A488
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0031593 polyubiquitin modification-dependent protein binding
Biological Process
GO:0030970 retrograde protein transport, ER to cytosol
GO:0051228 mitotic spindle disassembly
GO:0051301 cell division
GO:0097352 autophagosome maturation
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol
GO:0034098 VCP-NPL4-UFD1 AAA ATPase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6chs, PDBe:6chs, PDBj:6chs
PDBsum6chs
PubMed29967539
UniProtG0S6Y2

[Back to BioLiP]