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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF AN ACETATE KINASE FROM MYCOBACTERIUM SMEGMATIS BOUND TO AMP AND SULFATE

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   21 Dec 12 (Deposition) - 16 Jan 13 (Release) - 22 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Proprionate Kinase, Atp-Dependent, Metabolic Intermediate Biosynthesis, Acetyl-Coa Biosynthesis, Hydrolysis, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Transferase (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 - ACETATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAVA0421
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ACKA, MSMEG_0784, MSMEI_0768
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS
	Organism Taxid	:	246196
	Strain	:	ATCC 700084 / MC(2)155
	Synonym	:	ACETOKINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:72 , HIS A:104 , HIS A:161 , GLY A:193 , ARG A:222 , EDO A:404 , HOH A:811 , HOH A:826	BINDING SITE FOR RESIDUE SO4 A 401
2	AC2	SOFTWARE	GLY A:191 , ASN A:192 , ASP A:263 , PHE A:264 , ARG A:265 , ALA A:310 , GLY A:311 , VAL A:312 , ASN A:315 , VAL A:316 , HOH A:701 , HOH A:811 , HOH A:824	BINDING SITE FOR RESIDUE AMP A 402
3	AC3	SOFTWARE	GLU A:181 , SER A:182 , ASN A:184 , ALA A:200 , GLY A:201 , ARG A:302 , HOH A:776	BINDING SITE FOR RESIDUE EDO A 403
4	AC4	SOFTWARE	ARG A:72 , VAL A:74 , HIS A:104 , ASP A:129 , PHE A:160 , HIS A:161 , MET A:209 , ARG A:222 , SO4 A:401	BINDING SITE FOR RESIDUE EDO A 404
5	AC5	SOFTWARE	ARG B:72 , HIS B:104 , HIS B:161 , GLY B:193 , ARG B:222 , EDO B:403 , HOH B:782 , HOH B:784 , HOH B:820	BINDING SITE FOR RESIDUE SO4 B 401
6	AC6	SOFTWARE	GLY B:191 , ASN B:192 , ASP B:263 , PHE B:264 , ARG B:265 , ALA B:310 , GLY B:311 , VAL B:312 , ASN B:315 , VAL B:316 , HOH B:781 , HOH B:782 , HOH B:784 , HOH B:821	BINDING SITE FOR RESIDUE AMP B 402
7	AC7	SOFTWARE	ARG B:72 , VAL B:74 , HIS B:104 , PHE B:160 , HIS B:161 , MET B:209 , ARG B:222 , SO4 B:401	BINDING SITE FOR RESIDUE EDO B 403

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

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

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

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

(no "Exon" information available for 4IJN)

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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4ijna1 A:1-178 automated matches                                                                                                                                                 d4ijna2 A:179-376 automated matches                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeee......eeeeeee.........hhhhhhhhhhhhhhhh..hhhhh.eeeeeeee..........ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeee.hhhhh..hhhhhh...hhhhhhhh.......hhhhhhhhhhhhhhhh..hhhh.eeeeeee...eeeeeee..eeeee...................hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.hhhhh...hhhhhhh.....ee........eeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ijn A   1 MVTVLVVNSGSSSLKYAVVRPASGEFLADGIIEEIGSGAVPDHDAALRAAFDELAAAGLHLEDLDLKAVGHRMVHGGKTFYKPSVVDDELIAKARELSPLAPLHNPPAIKGIEVARKLLPDLPHIAVFDTAFFHDLPAPASTYAIDRELAETWHIKRYGFHGTSHEYVSQQAAIFLDRPLESLNQIVLHLGNGASASAVAGGKAVDTSMGLTPMEGLVMGTRSGDIDPGVIMYLWRTAGMSVDDIESMLNRRSGVLGLGGASDFRKLRELIESGDEHAKLAYDVYIHRLRKYIGAYMAVLGRTDVISFTAGVGENVPPVRRDALAGLGGLGIEIDDALNSAKSDEPRLISTPDSRVTVLVVPTNEELAIARACVGV 376
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370

Chain B from PDB  Type:PROTEIN  Length:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4ijnb1 B:2-178 automated matches                                                                                                                                                d4ijnb2 B:179-376 automated matches                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee....eeeeeeee.........hhhhhhhhhhhhhhhh..hhhhh.eeeeeeee..........ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeee.hhhhh..hhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhh..hhhh.eeeeeee...eeeeeee..eeeee...................hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.hhhhh...hhhhhhh.....ee........eeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ijn B   2 VTVLVVNSGSSSLKYAVVRPASGEFLADGIIEEIGSGAVPDHDAALRAAFDELAAAGLHLEDLDLKAVGHRMVHGGKTFYKPSVVDDELIAKARELSPLAPLHNPPAIKGIEVARKLLPDLPHIAVFDTAFFHDLPAPASTYAIDRELAETWHIKRYGFHGTSHEYVSQQAAIFLDRPLESLNQIVLHLGNGASASAVAGGKAVDTSMGLTPMEGLVMGTRSGDIDPGVIMYLWRTAGMSVDDIESMLNRRSGVLGLGGASDFRKLRELIESGDEHAKLAYDVYIHRLRKYIGAYMAVLGRTDVISFTAGVGENVPPVRRDALAGLGGLGIEIDDALNSAKSDEPRLISTPDSRVTVLVVPTNEELAIARACVGV 376
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: automated matches (111)

Protein domain: automated matches (111)

Mycobacterium smegmatis [TaxId: 246196] (1)

1a	d4ijna1	A:1-178
1b	d4ijna2	A:179-376
1c	d4ijnb1	B:2-178
1d	d4ijnb2	B:179-376

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ijn)

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	4ijn
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	ACKA_MYCS2 \| A0QQK1
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	2.7.2.1
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(no "Entries Sharing at Least One Protein Chain" available for 4IJN)

3p4i	ACKA M. AVIUM
3r9p	ACKA M. PARATUBERCULOSIS
4dq8	ACKA M. MARINUM RELATED ID: MYSMA.00640.A RELATED DB: TARGETTRACK

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

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