Structure of PDB 2ynm Chain B Binding Site BS04

Receptor Information
>2ynm Chain B (length=268) Species: 1219 (Prochlorococcus marinus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GALVIAVYGKGGIGKSTTSSNLSAAFSKLGKKVLQIGCDPKHDSTFTLTH
KMVPTVIDILEEVDFHSEELRPQDFMFEGFNGVQCVESGGPPAGTGCGGY
VTGQTVKLLKEHHLLEDTDVVIFDVLGDVVCGGFAAPLQHANYCLIVTAN
DFDSIFAMNRIVAAINAKAKNYKVRLGGVIANRSAELDQIEKFNEKTGLK
TMAHFRNVDAIRRSRLKKCTIFEMDPEEEGVLEVQNEYLSLAKKMIDNVE
PLEAEPLKDREIFDLLGF
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 chain2ynm Chain B Residue 1299 [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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PDB2ynm Structure of Adp-Aluminium Fluoride-Stabilized Protochlorophyllide Oxidoreductase Complex.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G39 G41 K42 S43 T44 N209 R210 R233 N234 V235 I238 R239
Binding residue
(residue number reindexed from 1)		G12 G14 K15 S16 T17 N182 R183 R206 N207 V208 I211 R212
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K37 K42 K68 D155
Catalytic site (residue number reindexed from 1) K10 K15 K41 D128
Enzyme Commision number 1.3.7.7: ferredoxin:protochlorophyllide reductase (ATP-dependent).
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
GO:0016636 oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
GO:0016730 oxidoreductase activity, acting on iron-sulfur proteins as donors
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0015979 photosynthesis
GO:0015995 chlorophyll biosynthetic process
GO:0019685 photosynthesis, dark reaction
GO:0036068 light-independent chlorophyll biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:2ynm, PDBe:2ynm, PDBj:2ynm
PDBsum2ynm
PubMed23341615
UniProtQ7VD39|CHLL_PROMA Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (Gene Name=chlL)

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