4NBJ - 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)

Biological Unit 4 (Jmol Viewer)

Title :   D-AMINOACYL-TRNA DEACYLASE (DTD) FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH D-TYROSYL-3'-AMINOADENOSINE AT 2.20 ANGSTROM RESOLUTION

Authors :   S. Ahmad, S. B. Routh, V. Kamarthapu, R. Sankaranarayanan

Date :   23 Oct 13 (Deposition) - 18 Dec 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: G,H  (1x)

Keywords :   Dtd, Deacylase, Dtd-Like, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ahmad, S. B. Routh, V. Kamarthapu, J. Chalissery, S. Muthukumar, T. Hussain, S. P. Kruparani, M. V. Deshmukh, R. Sankaranarayanan
Mechanism Of Chiral Proofreading During Translation Of The Genetic Code.
Elife V. 2 01519 2013
PubMed-ID: 24302572 | Reference-DOI: 10.7554/ELIFE.01519

Molecule 1 - D-TYROSYL-TRNA(TYR) DEACYLASE
	Chains	:	A, B, C, D, E, F, G, H
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DTD, PF11_0095
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	D3Y	8	Ligand/Ion	3'-DEOXY-3'-(D-TYROSYLAMINO)ADENOSINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	D3Y	2	Ligand/Ion	3'-DEOXY-3'-(D-TYROSYLAMINO)ADENOSINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	D3Y	2	Ligand/Ion	3'-DEOXY-3'-(D-TYROSYLAMINO)ADENOSINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	D3Y	2	Ligand/Ion	3'-DEOXY-3'-(D-TYROSYLAMINO)ADENOSINE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	D3Y	2	Ligand/Ion	3'-DEOXY-3'-(D-TYROSYLAMINO)ADENOSINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:41 , ILE A:43 , SER A:87 , GLN A:88 , PHE A:89 , LYS A:107 , PHE A:137 , GLY A:138 , ASN A:139 , TRP B:72 , GLY B:149 , PRO B:150	BINDING SITE FOR RESIDUE D3Y A 201
2	AC2	SOFTWARE	GLY A:149 , PRO A:150 , LEU B:41 , ILE B:43 , SER B:87 , GLN B:88 , PHE B:89 , LYS B:107 , PHE B:137 , GLY B:138	BINDING SITE FOR RESIDUE D3Y B 201
3	AC3	SOFTWARE	LEU C:41 , ILE C:43 , SER C:87 , GLN C:88 , PHE C:89 , LYS C:107 , PHE C:137 , GLY C:138 , ASN C:139 , TRP D:72 , GLY D:149 , PRO D:150	BINDING SITE FOR RESIDUE D3Y C 201
4	AC4	SOFTWARE	GLY C:149 , PRO C:150 , LEU D:41 , ILE D:43 , SER D:87 , GLN D:88 , PHE D:89 , LYS D:107 , PHE D:137 , GLY D:138 , TYR D:140	BINDING SITE FOR RESIDUE D3Y D 201
5	AC5	SOFTWARE	LEU E:41 , ILE E:43 , SER E:87 , GLN E:88 , PHE E:89 , LYS E:107 , PHE E:137 , GLY E:138 , ASN E:139 , MET E:141 , TRP F:72 , GLY F:149 , PRO F:150	BINDING SITE FOR RESIDUE D3Y E 201
6	AC6	SOFTWARE	PRO E:150 , LEU F:41 , ILE F:43 , SER F:87 , GLN F:88 , PHE F:89 , LYS F:107 , PHE F:137 , GLY F:138	BINDING SITE FOR RESIDUE D3Y F 201
7	AC7	SOFTWARE	LEU G:41 , ILE G:43 , SER G:87 , GLN G:88 , PHE G:89 , ALA G:106 , LYS G:107 , PHE G:137 , GLY G:138 , GLY H:149 , PRO H:150	BINDING SITE FOR RESIDUE D3Y G 201
8	AC8	SOFTWARE	GLY G:149 , PRO G:150 , LEU H:41 , ILE H:43 , SER H:87 , GLN H:88 , PHE H:89 , LYS H:107 , PHE H:137 , GLY H:138 , ASN H:139 , HOH H:349	BINDING SITE FOR RESIDUE D3Y H 201

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

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
7	Gly G:149	-	Pro G:150
8	Gly H:149	-	Pro H:150

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

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

(no "Exon" information available for 4NBJ)

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:154
                                                                                                                                                                                          
               SCOP domains d4nbja_ A: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbj A   1 MRVVIQRVKGAILSVRKENLEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10        27        37        47        57        67        77        87        97       107       117       127       137       147       157    
                                             19|                                                                                                                                      
                                              27

Chain B from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains d4nbjb_ B: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbj B   1 MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDINL 162
                                    10      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158    
                                           17|                                                                                                                                        
                                            26

Chain C from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains d4nbjc_ C: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbj C   1 MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158  
                                           17|                                                                                                                                      
                                            26

Chain D from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains d4nbjd_ D: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbj D   1 MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDINL 162
                                    10      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158    
                                           17|                                                                                                                                        
                                            26

Chain E from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains d4nbje_ E: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbj E   1 MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158  
                                           17|                                                                                                                                      
                                            26

Chain F from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains d4nbjf_ F: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eeeeee..eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.hhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbj F   1 MRVVIQRVKGAILSVRKLEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDINL 162
                                    10      ||29        39        49        59        69        79        89        99       109       119       129       139       149       159   
                                           17|                                                                                                                                       
                                            27

Chain G from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains d4nbjg_ G: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eeeee..eeeeeee.....hhhhhhhhhhhhhhh..................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbj G   1 MRVVIQRVKGAILSVRKEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDINL 162
                                    10      ||30        40        50        60       |71        81        91       101       111       121       131       141       151       161 
                                           17|                                      68|                                                                                            
                                            28                                       70

Chain H from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains d4nbjh_ H: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbj H   1 MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158  
                                           17|                                                                                                                                      
                                            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	d4nbja_	A:
1b	d4nbjb_	B:
1c	d4nbjc_	C:
1d	d4nbjd_	D:
1e	d4nbje_	E:
1f	d4nbjf_	F:
1g	d4nbjg_	G:
1h	d4nbjh_	H:

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

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

Asymmetric Unit(hide GO term definitions)

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 ]
		Gly G:149 - Pro G:150	[ RasMol ]
		Gly H:149 - Pro H:150	[ RasMol ]

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		Biological Unit 4	[ Jena3D ]

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	4nbj
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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