Structure of PDB 2d1r Chain A Binding Site BS01

Receptor Information
>2d1r Chain A (length=539) Species: 7051 (Nipponoluciola cruciata) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DENIVVGPKPFYPIEEGSAGTQLRKYMERYAKLGAIAFTNAVTGVDYSYA
EYLEKSCCLGKALQNYGLVVDGRIALCSENCEEFFIPVIAGLFIGVGVAP
TNEIYTLRELVHSLGISKPTIVFSSKKGLDKVITVQKTVTTIKTIVILDS
KVDYRGYQCLDTFIKRNTPPGFQASSFKTVEVDRKEQVALIMNSSGSTGL
PKGVQLTHENIVTRFSHARDPIYGNQVSPGTAVLTVVPFHHGFGMFTTLG
YLICGFRVVMLTKFDEETFLKTLQDYKCTSVILVPTLFAILNKSELLNKY
DLSNLVEIASGGAPLSKEVGEAVARRFNLPGVRQGYGLTETTSAIIITPE
GDDKPGASGKVVPLFKAKVIDLDTKKSLGPNRRGEVCVKGPMLMKGYVNN
PEATKELIDEEGWLHTGDIGYYDEEKHFFIVDRLKSLIKYKGYQVPPAEL
ESVLLQHPSIFDAGVAGVPDPVAGELPGAVVVLESGKNMTEKEVMDYVAS
QVSNAKRLRGGVRFVDEVPKGLTGKIDGRAIREILKKPV
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain2d1r Chain A Residue 1001 [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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PDB2d1r Structural basis for the spectral difference in luciferase bioluminescence.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		S200 S201 H247 G318 A319 P320 G341 Y342 G343 L344 T345 D424 K531
Binding residue
(residue number reindexed from 1)		S194 S195 H241 G312 A313 P314 G335 Y336 G337 L338 T339 D418 K525
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) S200 R220 H247 T345 E346 K445 Q450 K531
Catalytic site (residue number reindexed from 1) S194 R214 H241 T339 E340 K439 Q444 K525
Enzyme Commision number 1.13.12.7: firefly luciferase.
Gene Ontology
Molecular Function
GO:0004467 long-chain fatty acid-CoA ligase activity
GO:0004497 monooxygenase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
GO:0047077 Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity
Biological Process
GO:0001676 long-chain fatty acid metabolic process
GO:0008218 bioluminescence
GO:0046949 fatty-acyl-CoA biosynthetic process
Cellular Component
GO:0005777 peroxisome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2d1r, PDBe:2d1r, PDBj:2d1r
PDBsum2d1r
PubMed16541080
UniProtP13129|LUCI_NIPCR Luciferin 4-monooxygenase

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