Structure of PDB 3koy Chain D Binding Site BS02

Receptor Information
>3koy Chain D (length=728) Species: 1511 (Acetoanaerobium sticklandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQLRVNEKLDVENILKDLDKYTPKRRGWTWRQPAENLQMGPFIYKDASTP
LENSVALPSAKYFGDIDPQPLPVITTEIASGRFEDDIRRMRMAAWHGADH
IMVIRTAGQSHYDGLIEGTPQGIGGVPITRKQVRAQRKALDLIEEEVGRP
INYHSYVSGVAGPDIAVMFAEEGVNGAHQDPQYNVLYRNINMIRSFIDAC
ESKTIMAWADMAQIDGAHNANATAREAWKVMPELMVQHALNSIFSLKVGM
KKSNICLSTVPPTAPPAPSMYLDLPYAVALREMFEGYRMRAQMNTKYMEA
STREATVTHVLNLLISKLTRADIQSTITPDEGRNVPWHIYNIEACDTAKQ
ALIGMDGLMDMVQLKREGVLGDTVRELKERAVLFMEEIIEAGGYFNAVEQ
GFFVDSGYYPERNGDGIARQINGGIGAGTVFERDEDYMAPVTAHFGYNNV
KQYDEALVSEPSKLIDGCTLEVPEKIVYIDELDENDNVNVRMEETKEFRS
MIKPEVEWQADGTVLLTMFLPTSKRVAEFAAIEFAKKMNLEEVEVINREV
MQEAEGTRIELKGRVPFSIDINSLVIPPILSEDEIREDIEKTPLKIVAAT
VGEDEHSVGLREVIDIKHGGIEKYGVEVHYLGTSVPVEKLVDAAIELKAD
AILASTIISHDDIHYKNMKRIHELAVEKGIRDKIMIGCGGTQVTPEVAVK
QGVDAGFGRGSKGIHVATFLVKKRREMR
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 chain3koy Chain D Residue 1801 [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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PDB3koy Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		E617 H618 S619 V620 G621 V625 A666 S667 I669 S671 G701 G702 T703 G720 S723
Binding residue
(residue number reindexed from 1)		E605 H606 S607 V608 G609 V613 A654 S655 I657 S659 G689 G690 T691 G708 S711
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y187 H225 R297 K629
Catalytic site (residue number reindexed from 1) Y183 H218 R290 K617
Enzyme Commision number 5.4.3.5: D-ornithine 4,5-aminomutase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016853 isomerase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
GO:0046983 protein dimerization activity
GO:0047831 D-ornithine 4,5-aminomutase activity

View graph for
Molecular Function
External links
PDB RCSB:3koy, PDBe:3koy, PDBj:3koy
PDBsum3koy
PubMed20106986
UniProtE3PY95|OAME_ACESD D-ornithine 4,5-aminomutase subunit beta (Gene Name=oraE)

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