3KOD - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   DTD FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH D-SERINE

Authors :   Y. Manickam, T. K. Bhatt, A. Sharma

Date :   13 Nov 09 (Deposition) - 08 Dec 09 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   Dtd, Deacylase, D-Serine, D-Amino Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. K. Bhatt, M. Yogavel, S. Wydau, R. Berwal, A. Sharma
Ligand-Bound Structures Provide Atomic Snapshots For The Catalytic Mechanism Of D-Amino Acid Deacylase
J. Biol. Chem. V. 285 5917 2010
PubMed-ID: 20007323 | Reference-DOI: 10.1074/JBC.M109.038562

Molecule 1 - D-TYROSYL-TRNA(TYR) DEACYLASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DTD
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	DSN	4	Ligand/Ion	D-SERINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DSN	1	Ligand/Ion	D-SERINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	DSN	3	Ligand/Ion	D-SERINE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	DSN	-1	Ligand/Ion	D-SERINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:7 , ASN B:66 , THR B:71 , TRP B:72	BINDING SITE FOR RESIDUE DSN B 165
2	AC2	SOFTWARE	TRP C:72 , TYR D:140	BINDING SITE FOR RESIDUE DSN C 165
3	AC3	SOFTWARE	PHE D:89 , PRO D:109 , GLY D:138	BINDING SITE FOR RESIDUE DSN D 165
4	AC4	SOFTWARE	ASN C:66 , ARG D:16	BINDING SITE FOR RESIDUE DSN D 166

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

Asymmetric Unit

No.	Residues
1	Gly A:149	-	Pro A:150
2	Gly B:149	-	Pro B:150
3	Gly C:149	-	Pro C:150
4	Gly D:149	-	Pro D:150
5	Gly E:149	-	Pro E:150
6	Gly F:149	-	Pro F:150

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

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

(no "Exon" information available for 3KOD)

Asymmetric 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:151
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
               SCOP domains d3koda_ A: autom         ated matches                                                                                                                            SCOP domains
               CATH domains 3kodA00 A:1-160           [code=3.50.80.10, no name defined]                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................---------......................hhhhhhhhhhhhhhh.........................hhhhhh..............hhhhhhhhhhhhhhhhhhhh................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kod A   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160
                                          16        26

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
               SCOP domains d3kodb_ B: automat    ed matches                                                                                                                                  SCOP domains
               CATH domains 3kodB00 B:1-161  [    code=3.50.80.10, no name defined]                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................----.........................hhhhhhhhhhhhhhh..........................hhhh...............hhhhhhhhhhhhhhhhhhh.hhh...........................hhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kod B   1 MRVVIQRVKGAILSVRKE----NEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10       | -  |     30        40        50        60        70        80        90       100       110       120       130       140       150       160 
                                            18   23

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains d3kodc_ C: automat    ed matches                                                                                                                                SCOP domains
               CATH domains 3kodC00 C:1-159  [    code=3.50.80.10, no name defined]                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................----.........................hhhhhhhhhhhhhhh.............hhhhh........hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh............................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kod C   1 MRVVIQRVKGAILSVRKE----NEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10       | -  |     30        40        50        60        70        80        90       100       110       120       130       140       150         
                                            18   23

Chain D from PDB  Type:PROTEIN  Length:151
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains d3kodd_ D: automa        ted matches                                                                                                                            SCOP domains
               CATH domains 3kodD00 D:1-159          [code=3.50.80.10, no name defined]                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................--------......................hhhhhhhhhhhhhhh..............hhhh.......hhhhh...............hhhhhhhhhhhhhhhhhhhh................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kod D   1 MRVVIQRVKGAILSVRK--------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10      |  -     |  30        40        50        60        70        80        90       100       110       120       130       140       150         
                                           17       26

Chain E from PDB  Type:PROTEIN  Length:147
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains d3kode_ E: auto            mated matches                                                                                                                        SCOP domains
               CATH domains 3kodE00 E:1-159              [code=3.50.80.10, no name defined]                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............------------....................hhhhhhhhhhhhhhh..............hhhh........hhhhh................hhhhhhhhhhhhhhhhhhhhhhh........................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kod E   1 MRVVIQRVKGAILSV------------EIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10    |    -       |30        40        50        60        70        80        90       100       110       120       130       140       150         
                                         15           28

Chain F from PDB  Type:PROTEIN  Length:151
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
               SCOP domains d3kodf_ F: autom         ated matches                                                                                                                            SCOP domains
               CATH domains 3kodF00 F:1-160           [code=3.50.80.10, no name defined]                                                                                                     CATH domains
           Pfam domains (1) -Tyr_Deacylase-3         kodF01 F:2-157                                                                                                                      --- Pfam domains (1)
           Pfam domains (2) -Tyr_Deacylase-3         kodF02 F:2-157                                                                                                                      --- Pfam domains (2)
           Pfam domains (3) -Tyr_Deacylase-3         kodF03 F:2-157                                                                                                                      --- Pfam domains (3)
           Pfam domains (4) -Tyr_Deacylase-3         kodF04 F:2-157                                                                                                                      --- Pfam domains (4)
           Pfam domains (5) -Tyr_Deacylase-3         kodF05 F:2-157                                                                                                                      --- Pfam domains (5)
           Pfam domains (6) -Tyr_Deacylase-3         kodF06 F:2-157                                                                                                                      --- Pfam domains (6)
         Sec.struct. author ................---------......................hhhhhhhhhhhhhhh..........................hhhhh................hhhhhhhhhhhhhhhhhh................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kod F   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160
                                          16        26

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: DTD-like (18)

Superfamily: DTD-like (18)

Family: automated matches (15)

Protein domain: automated matches (15)

Plasmodium falciparum [TaxId: 36329] (13)

1a	d3koda_	A:
1b	d3kodb_	B:
1c	d3kodc_	C:
1d	d3kodd_	D:
1e	d3kode_	E:
1f	d3kodf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: D-tyrosyl-trna(Tyr) Deacylase; Chain: A; (15)

Homologous Superfamily: [code=3.50.80.10, no name defined] (15)

Plasmodium falciparum. Organism_taxid: 36329. Strain: 3d7. (10)

1a	3kodC00	C:1-159
1b	3kodA00	A:1-160
1c	3kodD00	D:1-159
1d	3kodF00	F:1-160
1e	3kodB00	B:1-161
1f	3kodE00	E:1-159

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Tyr_Deacylase] (12)

Family: Tyr_Deacylase (12)

Plasmodium falciparum (isolate 3D7) (9)

1a	Tyr_Deacylase-3kodF01	F:2-157
1b	Tyr_Deacylase-3kodF02	F:2-157
1c	Tyr_Deacylase-3kodF03	F:2-157
1d	Tyr_Deacylase-3kodF04	F:2-157
1e	Tyr_Deacylase-3kodF05	F:2-157
1f	Tyr_Deacylase-3kodF06	F:2-157

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q8IIS0_PLAF7 | Q8IIS0)

molecular function
	GO:0051500	D-tyrosyl-tRNA(Tyr) deacylase activity	Catalysis of the reaction: D-tyrosyl-tRNA(Tyr) = D-tyrosine + tRNA(Tyr). Hydrolysis of the removal of D-tyrosine from tyrosine residues in charged tRNA.
	GO:0002161	aminoacyl-tRNA editing activity	The hydrolysis of an incorrectly aminoacylated tRNA.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0019478	D-amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
	GO:0006450	regulation of translational fidelity	Any process that modulates the ability of the translational apparatus to interpret the genetic code.
	GO:0006399	tRNA metabolic process	The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:149 - Pro A:150	[ RasMol ]
		Gly B:149 - Pro B:150	[ RasMol ]
		Gly C:149 - Pro C:150	[ RasMol ]
		Gly D:149 - Pro D:150	[ RasMol ]
		Gly E:149 - Pro E:150	[ RasMol ]
		Gly F:149 - Pro F:150	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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SAPs(SNPs)/Variants (0, 0)

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