Structure of PDB 3kp1 Chain D Binding Site BS02

Receptor Information
>3kp1 Chain D (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)		E617 H618 S619 V620 G621 V625 A666 S667 I669 I670 S671 G701 G702 T703 F719 G720 S723
Binding residue
(residue number reindexed from 1)		E603 H604 S605 V606 G607 V611 A652 S653 I655 I656 S657 G687 G688 T689 F705 G706 S709
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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