Structure of PDB 4q71 Chain B Binding Site BS01

Receptor Information
>4q71 Chain B (length=970) 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
RLMGNHFVLGETIEQALERGKPQKTRYSFDMLGEGARTAADARRYFDAYA
SAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVELVPQLLD
LAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQA
YQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPV
FTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGF
EFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGA
NSSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRN
SRGVEFGARTALDQLLTDVKAEIADATPDQAHAAVAAARAGFAGWSRTPA
GIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYY
AAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFPLAIFLGQVT
AALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAA
LTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADA
TALPEQVADWVVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAAREL
KIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVA
PHIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVH
SRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLSGTGPKAGGP
HYLARFATEQTVTINTAAAG
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 chain4q71 Chain B Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4q71 Kinetic and Structural Characterization of Tunnel-Perturbing Mutants in Bradyrhizobium japonicum Proline Utilization A.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D278 A279 Q312 R339 V341 K342 G343 A344 Y345 W346 F364 T365 R366 K367 T370 A393 T394 H395 N396 Y441 S466 F467
Binding residue
(residue number reindexed from 1)		D265 A266 Q299 R326 V328 K329 G330 A331 Y332 W333 F351 T352 R353 K354 T357 A380 T381 H382 N383 Y428 S453 F454
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) N658 K681 E758 C792 E884 A966
Catalytic site (residue number reindexed from 1) N639 K662 E739 C773 E865 A947
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:4q71, PDBe:4q71, PDBj:4q71
PDBsum4q71
PubMed25046425
UniProtQ89E26

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