Structure of PDB 5dyg Chain A Binding Site BS01

Receptor Information
>5dyg Chain A (length=446) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKR
REAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRI
HVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFK
VVETDPSPYCIVAPDTVIHCEGEPIKREDEEESWNEVGYDDIGGCRKQLA
QIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA
FFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKRE
KTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFD
REVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAAL
CSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSN
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-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)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[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)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5dyg Chain A Residue 800 [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]
PDB5dyg Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G207 G248 T249 G250 K251 T252 L253 I380 H384 G408 A409
Binding residue
(residue number reindexed from 1)		G193 G234 T235 G236 K237 T238 L239 I366 H370 G394 A395
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.6: vesicle-fusing ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity

View graph for
Molecular Function
External links
PDB RCSB:5dyg, PDBe:5dyg, PDBj:5dyg
PDBsum5dyg
PubMed26818443
UniProtP55072|TERA_HUMAN Transitional endoplasmic reticulum ATPase (Gene Name=VCP)

[Back to BioLiP]