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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH CMP-N3-OXIDE
 
Authors :  T. K. To, L. P. Kotra, E. F. Pai
Date :  15 Oct 12  (Deposition) - 14 Nov 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Barrel, Decarboxylase, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Purohit, E. Poduch, L. W. Wei, I. E. Crandall, T. To, K. C. Kain, E. F. Pai, L. P. Kotra
Novel Cytidine-Based Orotidine-5'-Monophosphate Decarboxylase Inhibitors With An Unusual Twist.
J. Med. Chem. V. 55 9988 2012
PubMed-ID: 22991951  |  Reference-DOI: 10.1021/JM301176R

(-) Compounds

Molecule 1 - URIDINE 5'-MONOPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 4.1.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 190-480
    Gene: UMPS, OK/SW-CL.21
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UMP SYNTHASE, OROTATE PHOSPHORIBOSYLTRANSFERASE, OPRT, OPRTASE, OROTIDINE 5'-PHOSPHATE DECARBOXYLASE, ODC, OMPDECASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
116B1Ligand/IonN-HYDROXYCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
2GOL6Ligand/IonGLYCEROL
3TKW2Ligand/Ion5-HYDROXYCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:53 , PHE A:118 , LEU A:119 , ASP A:149 , GOL A:302 , HOH A:435 , HOH A:504BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWARESER A:146 , ARG A:174 , GOL A:301 , HOH A:435BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWARELYS A:61 , PRO A:86 , GLU A:275 , ARG A:278 , HOH A:493BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWARESER A:68 , ASP A:70 , LYS A:92 , HIS A:94 , ASP A:123 , LYS A:125 , MET A:182 , SER A:183 , ILE A:212 , PRO A:228 , GLN A:241 , TYR A:243 , GLY A:261 , ARG A:262 , HOH A:413 , HOH A:414 , HOH A:415 , HOH A:462 , HOH A:468 , ASP B:128 , ILE B:129 , THR B:132BINDING SITE FOR RESIDUE TKW A 304
5AC5SOFTWARESER A:68 , ASP A:70 , LYS A:92 , HIS A:94 , ASP A:123 , LYS A:125 , GLU A:181 , MET A:182 , SER A:183 , PRO A:228 , GLN A:241 , TYR A:243 , GLY A:261 , ARG A:262 , HOH A:413 , HOH A:414 , HOH A:415 , HOH A:502 , ASP B:128 , ILE B:129 , THR B:132BINDING SITE FOR RESIDUE 16B A 305
6AC6SOFTWARELYS B:53 , ALA B:113 , LYS B:114 , PHE B:118 , LEU B:119 , ASP B:149 , HOH B:522BINDING SITE FOR RESIDUE GOL B 301
7AC7SOFTWARELEU B:232 , ALA B:234 , HOH B:458 , HOH B:512BINDING SITE FOR RESIDUE GOL B 302
8AC8SOFTWARESER B:37 , GLN B:59 , TYR B:285 , LEU B:286BINDING SITE FOR RESIDUE GOL B 303
9AC9SOFTWAREASP A:128 , ILE A:129 , THR A:132 , SER B:68 , ASP B:70 , LYS B:92 , HIS B:94 , LYS B:125 , MET B:182 , SER B:183 , ILE B:212 , PRO B:228 , GLN B:231 , GLN B:241 , TYR B:243 , GLY B:261 , ARG B:262 , HOH B:401 , HOH B:404 , HOH B:420 , HOH B:421 , HOH B:482BINDING SITE FOR RESIDUE TKW B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HKP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HKP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HKP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HKP)

(-) Exons   (0, 0)

(no "Exon" information available for 4HKP)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh...hhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhh...eeeee...........eeee.......ee.....ee.hhhhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hkp A  35 ELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRLG 290
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.eeeehhhhh...hhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhh...hhhhh..eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhh...eeeee...........eeee.................hhhhhhh.....eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hkp B  35 ELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRLG 290
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4HKP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HKP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HKP)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hkp
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  UMPS_HUMAN | P11172
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  4.1.1.23
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UMPS_HUMAN | P11172: 2eaw 2jgy 2p1f 2qcc 2qcd 2qce 2qcf 2qcg 2qch 2qcl 2qcm 2qcn 2v30 2wns 3bgg 3bgj 3bk0 3bvj 3dbp 3ewu 3eww 3ewx 3ewy 3ewz 3ex1 3ex2 3ex3 3ex4 3ex6 3g3d 3g3m 3l0k 3l0n 3mi2 3mo7 3mw7 4hib

(-) Related Entries Specified in the PDB File

4hib