Structure of PDB 1eex Chain A Binding Site BS01

Receptor Information

>1eex Chain A (length=551) Species: 571 (Klebsiella oxytoca)

MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTE
LDGKPVSDFDLIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSE
IVPLTTAMTPAKIVEVVSHMNVVEMMMAMQKMRARRTPSQQAHVTNVKDN
PVQIAADAAEGAWRGFDEQETTVAVARYAPFNAIALLVGSQVGRPGVLTQ
CSLEEATELKLGMLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLASSYA
SRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSV
SCIGVPSAVPSGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLL
MQFLPGTDFISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGL
RPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMPE
RNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGD
YLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDP
N

Ligand information

• Ligand ID: COY
• InChI: InChI=1S/C62H92N13O14P.C10H14N5.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;1-2-3-4-5-15-7-14-8-9(11)12-6-13-10(8)15;/h20-21,23,28,31,34-37,41-42,52-57,76,84H,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);6-7H,1-5H2,(H2,11,12,13);/q-4;;+5/b38-23-,50-32-,51-33-;;/t31-,34-,35-,36-,37+,41-,42+,52-,53-,54+,55+,56-,57+,59-,60+,61+,62+;;/m1../s1
• InChIKey: KWGNLVVAVJCVFN-OGKXECBZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O3)CO)O[P@@](=O)(O)O[C@H](C)CNC(=O)CC[C@@]4([C@H]([C@@H]5[C@]6([C@@]([C@@H](C7=C([C@H]8[C@@]([C@@H](C9=CC1C([C@@H](C2=C(C4[N-]5[Co+2](N89)(N12)(N76)CCCCCn1cnc2c1ncnc2N)C)CCC(=O)N)(C)C)CCC(=O)N)(C)CC(=O)N)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
  CACTVS 3.385: C[CH](CNC(=O)CC[C]1(C)[CH](CC(N)=O)[CH]2[N-][CH]1C(=C3[CH](CCC(N)=O)C(C)(C)[CH]4C=C5[CH](CCC(N)=O)[C](C)(CC(N)=O)[CH]6[N]5[Co++](CCCCCn7cnc8c(N)ncnc78)([N]34)[N]9C(=C6C)[CH](CCC(N)=O)[C](C)(CC(N)=O)[C]29C)C)O[P](O)(=O)O[CH]%10[CH](O)[CH](O[CH]%10CO)n%11cnc%12cc(C)c(C)cc%11%12
  OpenEye OEToolkits 2.0.7: Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=C(C8C(C(C9=CC1C(C(C2=C(C4[N-]5[Co+2](N12)(N89)(N76)CCCCCn1cnc2c1ncnc2N)C)CCC(=O)N)(C)C)CCC(=O)N)(C)CC(=O)N)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
  CACTVS 3.385: C[C@H](CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)[C@H]2[N-][C@H]1C(=C3[C@@H](CCC(N)=O)C(C)(C)[C@@H]4C=C5[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)[C@H]6[N@@]5[Co++](CCCCCn7cnc8c(N)ncnc78)([N@@]34)[N@@]9C(=C6C)[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)[C@]29C)C)O[P](O)(=O)O[C@H]%10[C@@H](O)[C@H](O[C@@H]%10CO)n%11cnc%12cc(C)c(C)cc%11%12
• Formula: C72 H106 Co N18 O14 P
• Name: CO-(ADENIN-9-YL-PENTYL)-COBALAMIN
• PDB chain: 1eex Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1eex How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): T172 E205 T222 S224 T259 S260 G261 Q267 M268 V300 S301 M373 F374 A375
• Binding residue (residue number reindexed from 1): T172 E205 T222 S224 T259 S260 G261 Q267 M268 V300 S301 M373 F374 A375
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Q141 H143 E170 E221 Q296 D335 S362
• Catalytic site (residue number reindexed from 1): Q141 H143 E170 E221 Q296 D335 S362
• Enzyme Commision number: 4.2.1.28: propanediol dehydratase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0016829 lyase activity
• GO:0016836 hydro-lyase activity
• GO:0031419 cobalamin binding
• GO:0046872 metal ion binding
• GO:0050215 propanediol dehydratase activity

External links

• PDB: RCSB:1eex, PDBe:1eex, PDBj:1eex
• PDBsum: 1eex
• PubMed: 10903944
• UniProt: Q59470