Structure of PDB 5ysn Chain A Binding Site BS01

Receptor Information
>5ysn Chain A (length=453) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLKTTLFGNVYQFKDVKEVLAKANELRSGDVLAGVAAASSQERVAAKQV
LSEMTVADIRNNPVIAYEDDCVTRLIQDDVNETAYNQIKNWSISELREYV
LSDETSVDDIAFTRKGLTSEVVAAVAKICSNADLIYGAKKMPVIKKANTT
IGIPGTFSARLQPNDTRDDVQSIAAQIYEGLSFGVGDAVIGVNPVTDDVE
NLSRVLDTIYGVIDKFNIPTQGCVLAHVTTQIEAIRRGAPGGLIFQSICG
SEKGLKEFGVELAMLDEARAVGAEFNRIAGENCLYFETGQGSALSAGANF
GADQVTMEARNYGLARHYDPFIVNTVVGFIGPEYLYNDRQIIRAGLEDHF
MGKLSGISMGCDCCYTNHADADQNLNENLMILLATAGCNYIMGMPLGDDI
MLNYQTTAFHDTATVRQLLNLRPSPEFERWLESMGIMANGRLTKRAGDPS
LFF
Ligand information
Ligand IDB12
InChIInChI=1S/C62H90N13O14P.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;/h20-21,23,28,31,34-37,41,52-53,56-57,72,76,84H,12-19,22,24-27H2,1-11H3,(H2,63,77)(H2,64,78)(H2,65,79)(H2,66,80)(H2,67,81)(H2,68,82)(H,69,83)(H,85,86);/q;+2/b42-23-,50-32-,55-33-;/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1
InChIKeyLKVIQTCSMMVGFU-DWSMJLPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89[N]5=C4C(=C1[NH]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
CACTVS 3.370[Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C](C)([CH]8N|3=C(C(=C4[CH](CCC(N)=O)C5(C)C)C)[C](C)(CCC(=O)NC[CH](C)O[P](O)(=O)O[CH]9[CH](O)[CH](O[CH]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[CH]8CC(N)=O)[C](C)(CC(N)=O)[CH]7CCC(N)=O)[C](C)(CC(N)=O)[CH]6CCC(N)=O
CACTVS 3.370[Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C@@](C)([C@@H]8N|3=C(C(=C4[C@@H](CCC(N)=O)C5(C)C)C)[C@](C)(CCC(=O)NC[C@@H](C)O[P](O)(=O)O[C@H]9[C@@H](O)[C@H](O[C@@H]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[C@H]8CC(N)=O)[C@@](C)(CC(N)=O)[C@@H]7CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O
FormulaC62 H89 Co N13 O14 P
NameCOBALAMIN
ChEMBL
DrugBank
ZINC
PDB chain5ysn Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ysn Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Resolution2.001 Å
Binding residue
(original residue number in PDB)		P194 A226 Q246 S247 F258 S295 F329 I330 M401 L402
Binding residue
(residue number reindexed from 1)		P194 A226 Q246 S247 F258 S295 F329 I330 M401 L402
Annotation score1
Enzymatic activity
Enzyme Commision number 4.3.1.7: ethanolamine ammonia-lyase.
Gene Ontology
Molecular Function
GO:0008851 ethanolamine ammonia-lyase activity
GO:0016829 lyase activity
GO:0031419 cobalamin binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0046336 ethanolamine catabolic process
Cellular Component
GO:0005829 cytosol
GO:0009350 ethanolamine ammonia-lyase complex
GO:0031469 bacterial microcompartment
GO:0031471 ethanolamine degradation polyhedral organelle

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ysn, PDBe:5ysn, PDBj:5ysn
PDBsum5ysn
PubMed29797764
UniProtP0AEJ6|EUTB_ECOLI Ethanolamine ammonia-lyase large subunit (Gene Name=eutB)

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