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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE CDD FROM MYCOBACTERIUM MARINUM
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 May 12  (Deposition) - 23 May 12  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Mycobacterium, Ortholog, Cytidine, Uridine, Zinc Binding Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - CYTIDINE DEAMINASE CDD
    Chains: A, B, C, D
    EC Number: 3.5.4.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CDD, MMAR_1204
    Organism Scientific: MYCOBACTERIUM MARINUM
    Organism Taxid: 216594
    Strain: ATCC BAA-535 / M

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:56 , CYS A:89 , CYS A:92 , HOH A:323BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS B:56 , CYS B:89 , CYS B:92 , HOH B:325BINDING SITE FOR RESIDUE ZN B 201
3AC3SOFTWARECYS C:56 , CYS C:89 , CYS C:92 , HOH C:335BINDING SITE FOR RESIDUE ZN C 201
4AC4SOFTWARECYS D:56 , CYS D:89 , CYS D:92 , HOH D:328BINDING SITE FOR RESIDUE ZN D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F3W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F3W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F3W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F3W)

(-) Exons   (0, 0)

(no "Exon" information available for 4F3W)

(-) 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:119
                                                                                                                                                       
               SCOP domains d4f3wa_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...ee......eehhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3w A   4 IDWKQLRDKATQVAAGAYAPYSRFPVGAAALVDDGRVVTGCNVENVSYGLALCAECGVVCALHATGGGRLVALACVDGRGAPLMPCGRCRQLLFEHGGPELLVDHLAGPRRLGDLLPEP 122
                                    13        23        33        43        53        63        73        83        93       103       113         


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d4f3wb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhh...ee......eehhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3w B   2 PDIDWKQLRDKATQVAAGAYAPYSRFPVGAAALVDDGRVVTGCNVENVSYGLALCAECGVVCALHATGGGRLVALACVDGRGAPLMPCGRCRQLLFEHGGPELLVDHLAGPRRLGDLLPEP 122
                                    11        21        31        41        51        61        71        81        91       101       111       121 


Chain C from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains d4f3wc_ C: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...ee......eehhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4f3w C   4 IDWKQLRDKATQVAAGAYAPYSRFPVGAAALVDDGRVVTGCNVENVSYGLALCAECGVVCALHATGGGRLVALACVDGRGAPLMPCGRCRQLLFEHGGPELLVDHLAGPRRLGDLLPEP 122
                                    13        23        33        43        53        63        73        83        93       103       113         


Chain D from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4f3wd_ D: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhh...ee......eehhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f3w D   3 DIDWKQLRDKATQVAAGAYAPYSRFPVGAAALVDDGRVVTGCNVENVSYGLALCAECGVVCALHATGGGRLVALACVDGRGAPLMPCGRCRQLLFEHGGPELLVDHLAGPRRLGDLLPEP 122
                                    12        22        32        42        52        62        72        82        92       102       112       122
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F3W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F3W)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3ijf CYTIDINE DEAMINASE FROM M. TUBERCULOSIS
3mpz CYTIDINE DEAMINASE FROM M. SMEGMATIS RELATED ID: MYMAA.00495.A RELATED DB: TARGETTRACK
3r2n CYTIDINE DEAMINASE FROM M. LEPRAE