3CTO - JenaLib

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Biological Unit 12 (Jmol Viewer)

Biological Unit 13 (Jmol Viewer)

Biological Unit 14 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF M. TUBERCULOSIS YEFM ANTITOXIN

Authors :   P. Kumar, B. Issac, E. J. Dodson, J. P. Turkenberg, S. C. Mande

Date :   14 Apr 08 (Deposition) - 02 Dec 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x),E (1x)
Biol. Unit 4: A (1x),B (1x),C (1x),D (1x),E (1x)
Biol. Unit 5: A (1x),B (1x),C (1x),D (1x),E (1x)
Biol. Unit 6: A (1x),B (1x),C (1x),D (1x),E (1x)
Biol. Unit 7: A,B,D  (1x)
Biol. Unit 8: C (1x),E (1x)
Biol. Unit 9: C (1x),D (1x),E (1x)
Biol. Unit 10: A,B  (1x)
Biol. Unit 11: A (1x),C (1x),E (1x)
Biol. Unit 12: B,D  (1x)
Biol. Unit 13: A (1x),B (1x),D (1x)
Biol. Unit 14: C (1x),E (1x)

Keywords :   Homotetramer, Toxin Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kumar, B. Issac, E. J. Dodson, J. P. Turkenburg, S. C. Mande
Crystal Structure Of Mycobacterium Tuberculosis Yefm Antitoxin Reveals That It Is Not An Intrinsically Unstructured Protein
J. Mol. Biol. V. 383 482 2008
PubMed-ID: 18793646 | Reference-DOI: 10.1016/J.JMB.2008.08.067

Molecule 1 - UNCHARACTERIZED PROTEIN RV3357/MT3465
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	ANTITOXIN

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)
Biological Unit 4 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)
Biological Unit 5 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)
Biological Unit 6 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)
Biological Unit 7 (1x)	:	A	B		D
Biological Unit 8 (1x)	:			C (1x)		E (1x)
Biological Unit 9 (1x)	:			C (1x)	D (1x)	E (1x)
Biological Unit 10 (1x)	:	A	B
Biological Unit 11 (1x)	:	A (1x)		C (1x)		E (1x)
Biological Unit 12 (1x)	:		B		D
Biological Unit 13 (1x)	:	A (1x)	B (1x)		D (1x)
Biological Unit 14 (1x)	:			C (1x)		E (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 7 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 8 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 9 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 10 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 11 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 12 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 13 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 14 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:57 , ARG A:60 , ARG A:61 , ARG B:59 , ARG B:60 , LYS C:78	BINDING SITE FOR RESIDUE SO4 A 201
2	AC2	SOFTWARE	PHE C:13 , SER D:3 , ALA D:4 , SER D:5 , ARG D:30	BINDING SITE FOR RESIDUE SO4 D 202

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

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

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

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

(no "Exon" information available for 3CTO)

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:68
 aligned with RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:68
                                    10        20        30        40        50        60        
            RELJ_MYCTO    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVAR 68
               SCOP domains d3ctoa_ A: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3cto A  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVAR 68
                                    10        20        30        40        50        60

Chain A from PDB  Type:PROTEIN  Length:68
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:68
                                    10        20        30        40        50        60        
            RELJ_MYCTU    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVAR 68
               SCOP domains d3ctoa_ A: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3cto A  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVAR 68
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:83
 aligned with RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:83
                                    11        21        31        41        51        61        71        81   
            RELJ_MYCTO    2 SISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELR 84
               SCOP domains d3ctob_ B: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhh.....eeee.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  3cto B  1 SISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELR 83
                                    10        20        30        40        50        60        70        80

Chain B from PDB  Type:PROTEIN  Length:83
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:83
                                    11        21        31        41        51        61        71        81   
            RELJ_MYCTU    2 SISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELR 84
               SCOP domains d3ctob_ B: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhh.....eeee.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  3cto B  1 SISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELR 83
                                    10        20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
            RELJ_MYCTO    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREM 86
               SCOP domains d3ctoc_ C: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  3cto C  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREM 86
                                    10        20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
            RELJ_MYCTU    1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREM 86
               SCOP domains d3ctoc_ C: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  3cto C  1 MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREM 86
                                    10        20        30        40        50        60        70        80

Chain D from PDB  Type:PROTEIN  Length:65
 aligned with RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:65
                                    11        21        31        41        51        61     
            RELJ_MYCTO    2 SISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAV 66
               SCOP domains d3ctod_ D: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  3cto D  1 SISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAV 65
                                    10        20        30        40        50        60

Chain D from PDB  Type:PROTEIN  Length:65
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:65
                                    11        21        31        41        51        61     
            RELJ_MYCTU    2 SISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAV 66
               SCOP domains d3ctod_ D: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhhhh..eeee.....eeeeehhhhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  3cto D  1 SISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAV 65
                                    10        20        30        40        50        60

Chain E from PDB  Type:PROTEIN  Length:16
 aligned with RELJ_MYCTO | P9WF24 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:16
                                    83      
            RELJ_MYCTO   74 SAFTKSVDELREMAGG 89
               SCOP domains d3ctoe_ E:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  3cto E  1 SAFTKSVDELREMAGG 16
                                    10

Chain E from PDB  Type:PROTEIN  Length:16
 aligned with RELJ_MYCTU | P9WF25 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:16
                                    83      
            RELJ_MYCTU   74 SAFTKSVDELREMAGG 89
               SCOP domains d3ctoe_ E:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  3cto E  1 SAFTKSVDELREMAGG 16
                                    10

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) (23004)

Fold: YefM-like (5)

Superfamily: YefM-like (5)

Family: automated matches (3)

Protein domain: automated matches (3)

Mycobacterium tuberculosis [TaxId: 1773] (3)

1a	d3ctoa_	A:
1b	d3ctob_	B:
1c	d3ctoc_	C:
1d	d3ctod_	D:

Class: Peptides (792)

Fold: YefM fragments (1)

Superfamily: YefM fragments (1)

Family: YefM fragments (1)

Protein domain: YefM fragments (1)

Mycobacterium tuberculosis [TaxId: 1773] (1)

d3ctoe_

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (RELJ_MYCTO | P9WF24)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Chain A,B,C,D,E (RELJ_MYCTU | P9WF25)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

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	RELJ_MYCTO \| P9WF24	:	3d55 3oei
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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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