Structure of PDB 3kp0 Chain B Binding Site BS01

Receptor Information
>3kp0 Chain B (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 chain3kp0 Chain B Residue 1801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3kp0 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 A666 S667 I669 I670 S671 H672 G701 G702 T703 F719 G720 S723 V728
Binding residue
(residue number reindexed from 1)		E605 H606 S607 V608 G609 A654 S655 I657 I658 S659 H660 G689 G690 T691 F707 G708 S711 V716
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:3kp0, PDBe:3kp0, PDBj:3kp0
PDBsum3kp0
PubMed20106986
UniProtE3PY95|OAME_ACESD D-ornithine 4,5-aminomutase subunit beta (Gene Name=oraE)

[Back to BioLiP]