Structure of PDB 1mmf Chain L Binding Site BS01

Receptor Information
>1mmf Chain L (length=555) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKRSKRFAVLAQRPVNQDGLIGEWPEEGLIAMDSPFDPVSSVKVDNGLIV
ELDGKRRDQFDMIDRFIADYAINVERTEQAMRLEAVEIARMLVDIHVSRE
EIIAITTAITPAKAVEVMAQMNVVEMMMALQKMRARRTPSNQCHVTNLKD
NPVQIAADAAEAGIRGFSEQETTVGIARYAPFNALALLVGSQCGRPGVLT
QCSVEEATELELGMRGLTSYAETVSVYGTEAVFTDGDDTPWSKAFLASAY
ASRGLKMRYTSGTGSEALMGYSESKSMLYLESRCIFITKGAGVQGLQNGA
VSCIGMTGAVPSGIRAVLAENLIASMLDLEVASANDQTFSHSDIRRTART
LMQMLPGTDFIFSGYSAVPNYDNMFAGSNFDAEDFDDYNILQRDLMVDGG
LRPVTEAETIAIRQKAARAIQAVFRELGLPPIADEEVEAATYAHGSNEMP
PRNVVEDLSAVEEMMKRNITGLDIVGALSRSGFEDIASNILNMLRQRVTG
DYLQTSAILDRQFEVVSAVNDINDYQGPGTGYRISAERWAEIKNIPGVVQ
PDTIE
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 chain1mmf Chain E Residue 602 [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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PDB1mmf Crystal structure of substrate free form of glycerol dehydratase
Resolution2.5 Å
Binding residue
(original residue number in PDB)		T173 E206 L268 M269 M374 F375
Binding residue
(residue number reindexed from 1)		T173 E206 L268 M269 M374 F375
Annotation score1
Enzymatic activity
Enzyme Commision number 4.2.1.30: glycerol dehydratase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
GO:0031419 cobalamin binding
GO:0046405 glycerol dehydratase activity

View graph for
Molecular Function
External links
PDB RCSB:1mmf, PDBe:1mmf, PDBj:1mmf
PDBsum1mmf
PubMed12538056
UniProtQ59476

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