Structure of PDB 4q72 Chain B Binding Site BS01

Receptor Information
>4q72 Chain B (length=969) Species: 224911 (Bradyrhizobium diazoefficiens USDA 110) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKL
GGVEDMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFI
HHETKSTAFLVNASAWARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAM
RLMGNHFVLGETIEQALERGKPKTRYSFDMLGEGARTAADARRYFDAYAS
AIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVELVPQLLDL
AQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQAY
QKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPVF
TRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFE
FQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGAN
SSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNS
RGVEFGARTALDQLLTDVKAEIADATPDQAHAAVAAARAGFAGWSRTPAG
IRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYYA
AQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFPLAIFLGQVTA
ALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAAL
TAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADAT
ALPEQVADYVVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELK
IGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVAP
HIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVHS
RIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLSGTGPKAGGPH
YLARFATEQTVTINTAAAG
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 chain4q72 Chain B 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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PDB4q72 Kinetic and Structural Characterization of Tunnel-Perturbing Mutants in Bradyrhizobium japonicum Proline Utilization A.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D278 A279 Q312 R339 V341 K342 G343 A344 W346 F364 T365 R366 K367 T370 A393 T394 H395 N396 Y441 S466 F467
Binding residue
(residue number reindexed from 1)		D264 A265 Q298 R325 V327 K328 G329 A330 W332 F350 T351 R352 K353 T356 A379 T380 H381 N382 Y427 S452 F453
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) N658 K681 E758 C792 E884 A966
Catalytic site (residue number reindexed from 1) N638 K661 E738 C772 E864 A946
Enzyme Commision number 1.2.1.88: L-glutamate gamma-semialdehyde dehydrogenase.
1.5.5.2: proline dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
GO:0004657 proline dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0006560 proline metabolic process
GO:0006561 proline biosynthetic process
GO:0006562 proline catabolic process
GO:0010133 proline catabolic process to glutamate
Cellular Component
GO:0009898 cytoplasmic side of plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4q72, PDBe:4q72, PDBj:4q72
PDBsum4q72
PubMed25046425
UniProtQ89E26

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