Structure of PDB 3kp1 Chain B Binding Site BS03

Receptor Information
>3kp1 Chain B (length=726) Species: 1511 (Acetoanaerobium sticklandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRVNEKLDVENILKDLDKYTPKRRGWTWRQPAENLQMGPFIYKDASTPLE
NSVALPSAKYFGDIDPQPLPVITTEIASGRFEDDIRRMRMAAWHGADHIM
VIRTAGQSHYDGLIEGTPQGIGGVPITRKQVRAQRKALDLIEEEVGRPIN
YHSYVSGVAGPDIAVMFAEEGVNGAHQDPQYNVLYRNINMIRSFIDACES
KTIMAWADMAQIDGAHNANATAREAWKVMPELMVQHALNSIFSLKVGMKK
SNICLSTVPPTAPPAPSMYLDLPYAVALREMFEGYRMRAQMNTKYMEAST
REATVTHVLNLLISKLTRADIQSTITPDEGRNVPWHIYNIEACDTAKQAL
IGMDGLMDMVQLKREGVLGDTVRELKERAVLFMEEIIEAGGYFNAVEQGF
FVDSGYYPERNGDGIARQINGGIGAGTVFERDEDYMAPVTAHFGYNNVKQ
YDEALVSEPSKLIDGCTLEVPEKIVYIDELDENDNVNVRMEETKEFRSMI
KPEVEWQADGTVLLTMFLPTSKRVAEFAAIEFAKKMNLEEVEVINREVMQ
EAEGTRIELKGRVPFSIDINSLVIPPILSEDEIREDIEKTPLKIVAATVG
EDEHSVGLREVIDIKHGGIEKYGVEVHYLGTSVPVEKLVDAAIELKADAI
LASTIISHDDIHYKNMKRIHELAVEKGIRDKIMIGCGGTQVTPEVAVKQG
VDAGFGRGSKGIHVATFLVKKRREMR
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 chain3kp1 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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PDB3kp1 Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		Y116 I127
Binding residue
(residue number reindexed from 1)		Y110 I121
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y187 H225 R297 K629
Catalytic site (residue number reindexed from 1) Y181 H216 R288 K615
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:3kp1, PDBe:3kp1, PDBj:3kp1
PDBsum3kp1
PubMed20106986
UniProtE3PY95|OAME_ACESD D-ornithine 4,5-aminomutase subunit beta (Gene Name=oraE)

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