Structure of PDB 2nvu Chain B Binding Site BS02

Receptor Information
>2nvu Chain B (length=789) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQV
AATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYN
GKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFN
LQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIK
NKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTF
KGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKVAL
KSYEEEATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALA
AAQTNAAADWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLV
IGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPK
AEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRW
INGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECT
LELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDD
PEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVC
ATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNI
QFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEER
TRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain2nvu Chain B Residue 103 [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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PDB2nvu Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		G2057 D2079 M2080 D2081 K2103 K2126 I2127 Q2128 L2145 D2146
Binding residue
(residue number reindexed from 1)		G404 D426 M427 D428 K450 K473 I474 Q475 L492 D493
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K2021 D2146 C2216 T2217 A2219
Catalytic site (residue number reindexed from 1) K368 D493 C563 T564 A566
Enzyme Commision number 6.2.1.64: E1 NEDD8-activating enzyme.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008641 ubiquitin-like modifier activating enzyme activity
GO:0015144 carbohydrate transmembrane transporter activity
GO:0016874 ligase activity
GO:0019781 NEDD8 activating enzyme activity
GO:0019788 NEDD8 transferase activity
GO:0042802 identical protein binding
GO:0046982 protein heterodimerization activity
Biological Process
GO:0000278 mitotic cell cycle
GO:0006508 proteolysis
GO:0007113 endomitotic cell cycle
GO:0008643 carbohydrate transport
GO:0036211 protein modification process
GO:0043687 post-translational protein modification
GO:0045116 protein neddylation
GO:0051726 regulation of cell cycle
GO:0055085 transmembrane transport
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2nvu, PDBe:2nvu, PDBj:2nvu
PDBsum2nvu
PubMed17220875
UniProtQ8TBC4|UBA3_HUMAN NEDD8-activating enzyme E1 catalytic subunit (Gene Name=UBA3)

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