Structure of PDB 1xrs Chain B Binding Site BS01

Receptor Information
>1xrs Chain B (length=212) Species: 1511 (Acetoanaerobium sticklandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVQLSFTLPLKNNERSAEAAKQIALKMGLEEPSVVMQQSLDEEFTFFVVY
GNEILSMEETDEYIKENIGRKIVVVGASTGTDAHTVGIDAIMNMKGYAGH
YGLERYEMIDAYNLGSQVANEDFIKKAVELEADVLLVSQTVTQKNVHIQN
MTHLIELLEAEGLRDRFVLLCGGPRINNEIAKELGYDAGFGPGRFADDVA
TFAVKTLNDRMN
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 chain1xrs Chain B Residue 800 [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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PDB1xrs A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D131 A132 H133 T134 V135 I140 Y146 L185 V186 S187 T191 L219 C220 G221 G222 P223 F239 G240 P241 R243
Binding residue
(residue number reindexed from 1)		D82 A83 H84 T85 V86 I91 Y97 L136 V137 S138 T142 L170 C171 G172 G173 P174 F190 G191 P192 R194
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K144
Catalytic site (residue number reindexed from 1) K95
Enzyme Commision number 5.4.3.3: lysine 5,6-aminomutase.
Gene Ontology
Molecular Function
GO:0016853 isomerase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
GO:0046983 protein dimerization activity
GO:0047826 D-lysine 5,6-aminomutase activity

View graph for
Molecular Function
External links
PDB RCSB:1xrs, PDBe:1xrs, PDBj:1xrs
PDBsum1xrs
PubMed15514022
UniProtE3PRJ4|KAME_ACESD Lysine 5,6-aminomutase beta subunit (Gene Name=kamE)

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