Structure of PDB 1sez Chain B Binding Site BS01

Receptor Information
>1sez Chain B (length=465) Species: 4097 (Nicotiana tabacum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKRVAVIGAGVSGLAAAYKLKIHGLNVTVFEAEGKAGGKLRSVSQDGLIW
DEGANTMTESEGDVTFLIDSLGLREKQQFPLSQNKRYIARNGTPVLLPSN
PIDLIKSNFLSTGSKLQMLLEPILWSHESVSGFFQRHFGKEVVDYLIDPF
VAGTCGGDPDSLSMHHSFPELWNLEKRFGSVILGAIRSKLSKTSANKKRQ
RGSFSFLGGMQTLTDAICKDLREDELRLNSRVLELSCSCTEDSAIDSWSI
ISASPHKRQSEEESFDAVIMTAPLCDVKSMKIAKRGNPFLLNFIPEVDYV
PLSVVITTFKRENVKYPLEGFGVLVPSKEQQHGLKTLGTLFSSMMFPDRA
PNNVYLYTTFVGGSRNRELAKASRTELKEIVTSDLKQLLGAEGEPTYVNH
LYWSKAFPLYGHNYDSVLDAIDKMEKNLPGLFYAGNHRGGLSVGKALSSG
CNAADLVISYLESVS
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 chain1sez Chain B Residue 610 [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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PDB1sez Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		G20 G22 S24 F42 E43 A44 G50 K51 G65 A66 N67 T68 R263 V264 T303 A304 D308 A438 F439 N468 S474 V475
Binding residue
(residue number reindexed from 1)		G8 G10 S12 F30 E31 A32 G38 K39 G53 A54 N55 T56 R231 V232 T271 A272 D276 A406 F407 N436 S442 V443
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.3.4: protoporphyrinogen oxidase.
Gene Ontology
Molecular Function
GO:0004729 oxygen-dependent protoporphyrinogen oxidase activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0006782 protoporphyrinogen IX biosynthetic process
GO:0006783 heme biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1sez, PDBe:1sez, PDBj:1sez
PDBsum1sez
PubMed15057273
UniProtO24164|PPOM_TOBAC Protoporphyrinogen oxidase, mitochondrial (Gene Name=PPXII)

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