Structure of PDB 1dxl Chain B Binding Site BS01

Receptor Information
>1dxl Chain B (length=467) Species: 3888 (Pisum sativum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDENDVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPS
KALLHSSHMYHEAKHSFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIE
GLFKKNKVTYVKGYGKFVSPSEISVDTIEGENTVVKGKHIIIATGSDVKS
LPGVTIDEKKIVSSTGALALSEIPKKLVVIGAGYIGLEMGSVWGRIGSEV
TVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGVDTSGDGVKL
TVEPSAGGEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNE
RFSTNVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPG
VVYTNPEVASVGKTEEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKI
IAEKETDKILGVHIMAPNAGELIHEAAIALQYDASSEDIARVCHAHPTMS
EAIKEAAMATYDKPIHI
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain1dxl Chain B Residue 480 [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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PDB1dxl Interaction between the Lipoamide-Containing H-Protein and the Lipoamide Dehydrogenase (L-Protein) of the Glycine Decarboxylase Multienzyme System. 2. Crystal Structure of H- and L-Proteins
Resolution3.15 Å
Binding residue
(original residue number in PDB)		I12 G15 P16 G17 E36 K37 R38 G43 T44 C45 G49 C50 K54 Y117 G118 T147 G148 S167 I188 R277 D317 M323 L324 A325 H326
Binding residue
(residue number reindexed from 1)		I9 G12 P13 G14 E33 K34 R35 G40 T41 C42 G46 C47 K51 Y114 G115 T144 G145 S164 I185 R274 D314 M320 L321 A322 H323
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) L41 C45 C50 S53 Y187 E191 H447 H449 E454
Catalytic site (residue number reindexed from 1) L38 C42 C47 S50 Y184 E188 H444 H446 E451
Enzyme Commision number 1.8.1.4: dihydrolipoyl dehydrogenase.
Gene Ontology
Molecular Function
GO:0004148 dihydrolipoyl dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0050660 flavin adenine dinucleotide binding
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005960 glycine cleavage complex
GO:0045252 oxoglutarate dehydrogenase complex

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:1dxl, PDBe:1dxl, PDBj:1dxl
PDBsum1dxl
PubMed10806386
UniProtP31023|DLDH_PEA Dihydrolipoyl dehydrogenase, mitochondrial (Gene Name=LPD)

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