3R2N - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM MYCOBACTERIUM LEPRAE

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   14 Mar 11 (Deposition) - 23 Mar 11 (Release) - 22 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Tuberculosis, Cytidine Deaminase, Cda, Pyrimidine Salvage, Homotetramer, Drug Resistance, Zinc Binding Protein, Catalytic Zinc, 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

Molecule 1 - CYTIDINE DEAMINASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAVA0421
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CDD, MLBR02174
	Organism Scientific	:	MYCOBACTERIUM LEPRAE
	Organism Taxid	:	561304
	Strain	:	BR4923

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	1	Ligand/Ion	GLYCEROL
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:56 , CYS A:89 , CYS A:92 , EDO A:136	BINDING SITE FOR RESIDUE ZN A 135
2	AC2	SOFTWARE	GLU A:58 , LEU A:86 , PRO A:88 , CYS A:89 , ZN A:135 , HOH A:149	BINDING SITE FOR RESIDUE EDO A 136
3	AC3	SOFTWARE	CYS B:56 , CYS B:89 , CYS B:92 , EDO B:136	BINDING SITE FOR RESIDUE ZN B 135
4	AC4	SOFTWARE	VAL B:29 , CYS B:56 , GLU B:58 , CYS B:78 , MET B:87 , PRO B:88 , CYS B:89 , CYS B:92 , ZN B:135 , HOH B:143	BINDING SITE FOR RESIDUE EDO B 136
5	AC5	SOFTWARE	CYS C:56 , CYS C:89 , CYS C:92 , EDO C:136	BINDING SITE FOR RESIDUE ZN C 135
6	AC6	SOFTWARE	GLU C:58 , PRO C:88 , CYS C:89 , ZN C:135 , HOH C:138	BINDING SITE FOR RESIDUE EDO C 136
7	AC7	SOFTWARE	CYS D:56 , CYS D:89 , CYS D:92 , EDO D:136	BINDING SITE FOR RESIDUE ZN D 135
8	AC8	SOFTWARE	GLU D:58 , CYS D:78 , MET D:87 , PRO D:88 , CYS D:89 , CYS D:92 , ZN D:135	BINDING SITE FOR RESIDUE EDO D 136
9	AC9	SOFTWARE	ASP D:3 , ASN D:5 , PHE D:34	BINDING SITE FOR RESIDUE GOL D 137

(no "SS Bond" information available for 3R2N)

(no "Cis Peptide Bond" information available for 3R2N)

(no "SAP(SNP)/Variant" information available for 3R2N)

(no "PROSITE Motif" information available for 3R2N)

(no "Exon" information available for 3R2N)

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
 aligned with A0A0H3MRL9_M | A0A0H3MRL9 from UniProtKB/TrEMBL  Length:134

    Alignment length:119
                                    12        22        32        42        52        62        72        82        92       102       112         
         A0A0H3MRL9_M     3 DVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
               SCOP domains d3r2na_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...eeee..eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2n A   3 DVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
                                    12        22        32        42        52        62        72        82        92       102       112

Chain A from PDB  Type:PROTEIN  Length:119
 aligned with A0A0M3KKU2_M | A0A0M3KKU2 from UniProtKB/TrEMBL  Length:138

    Alignment length:119
                                    16        26        36        46        56        66        76        86        96       106       116         
         A0A0M3KKU2_M     7 DVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 125
               SCOP domains d3r2na_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...eeee..eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2n A   3 DVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
                                    12        22        32        42        52        62        72        82        92       102       112

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with A0A0H3MRL9_M | A0A0H3MRL9 from UniProtKB/TrEMBL  Length:134

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
         A0A0H3MRL9_M     1 MGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
               SCOP domains d3r2nb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...eeee..eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2n B   1 MGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with A0A0M3KKU2_M | A0A0M3KKU2 from UniProtKB/TrEMBL  Length:138

    Alignment length:121
                                    14        24        34        44        54        64        74        84        94       104       114       124 
         A0A0M3KKU2_M     5 MGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 125
               SCOP domains d3r2nb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...eeee..eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2n B   1 MGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:119
 aligned with A0A0H3MRL9_M | A0A0H3MRL9 from UniProtKB/TrEMBL  Length:134

    Alignment length:119
                                    12        22        32        42        52        62        72        82        92       102       112         
         A0A0H3MRL9_M     3 DVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
               SCOP domains d3r2nc_ C: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...eeee..eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2n C   3 DVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
                                    12        22        32        42        52        62        72        82        92       102       112

Chain C from PDB  Type:PROTEIN  Length:119
 aligned with A0A0M3KKU2_M | A0A0M3KKU2 from UniProtKB/TrEMBL  Length:138

    Alignment length:119
                                    16        26        36        46        56        66        76        86        96       106       116         
         A0A0M3KKU2_M     7 DVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 125
               SCOP domains d3r2nc_ C: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...eeee..eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2n C   3 DVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
                                    12        22        32        42        52        62        72        82        92       102       112

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with A0A0H3MRL9_M | A0A0H3MRL9 from UniProtKB/TrEMBL  Length:134

    Alignment length:122
                             1                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119  
         A0A0H3MRL9_M     - -MGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
               SCOP domains d3r2nd_ D: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...eeee..eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2n D   0 SMGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
                                     9        19        29        39        49        59        69        79        89        99       109       119

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with A0A0M3KKU2_M | A0A0M3KKU2 from UniProtKB/TrEMBL  Length:138

    Alignment length:122
                                    13        23        33        43        53        63        73        83        93       103       113       123  
         A0A0M3KKU2_M     4 SMGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 125
               SCOP domains d3r2nd_ D: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh...eeee..eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2n D   0 SMGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAECSMISALYATGGGRLVAVYCVDGNGDSLMPCGRCRQLLYEHGGPELKIMTPKGVQTMAQLLPQ 121
                                     9        19        29        39        49        59        69        79        89        99       109       119

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Cytidine deaminase-like (78)

Superfamily: Cytidine deaminase-like (76)

Family: automated matches (11)

Protein domain: automated matches (11)

Mycobacterium leprae [TaxId: 561304] (1)

1a	d3r2na_	A:
1b	d3r2nb_	B:
1c	d3r2nc_	C:
1d	d3r2nd_	D:

(no "CATH Domain" information available for 3R2N)

(no "Pfam Domain" information available for 3R2N)

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3R2N)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3r2n)

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3ijf	SAME PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS
3mpz	SAME PROTEIN FROM MYCOBACTERIUM SMEGMATIS RELATED ID: MYLEA.00495.A RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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