4IT1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ENOLASE PFL01_3283 (TARGET EFI-502286) FROM PSEUDOMONAS FLUORESCENS PF0-1 WITH BOUND MAGNESIUM, POTASSIUM AND TARTRATE

Authors :   Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washin A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H N. Al Obaidi, M. Stead, J. Love, J. A. Gerlt, S. C. Almo, Enzyme Functi Initiative (Efi)

Date :   17 Jan 13 (Deposition) - 30 Jan 13 (Release) - 30 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Isomerase, Dehydrogenase, Magnesium Binding Nadp, Structural Genomics, Enzyme Function Initiative, Efi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H. J. Imker, N. Al Obaidi, M. Stead, J. Love, J. A. Gerlt S. C. Almo
Crystal Structure Of Enolase Pfl01_3283 From Pseudomonas Fluorescens
To Be Published
PubMed: search

Molecule 1 - PUTATIVE GLUCARATE DEHYDRATASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Gene	:	PFL01_3283
	Organism Scientific	:	PSEUDOMONAS FLUORESCENS
	Organism Taxid	:	205922
	Strain	:	PF0-1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	BCT	1	Ligand/Ion	BICARBONATE ION
2	K	2	Ligand/Ion	POTASSIUM ION
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	TLA	4	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	BCT	-1	Ligand/Ion	BICARBONATE ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TLA	2	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	BCT	1	Ligand/Ion	BICARBONATE ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TLA	2	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	BCT	1	Ligand/Ion	BICARBONATE ION
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TLA	2	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:221 , GLU A:246 , ASN A:269 , HOH A:601 , HOH A:603 , HOH A:604	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	ASN A:20 , HIS A:25 , PRO A:99 , LYS A:193 , ASN A:223 , HIS A:349 , ARG A:404 , HOH A:604 , HOH A:639 , HOH A:647	BINDING SITE FOR RESIDUE TLA A 502
3	AC3	SOFTWARE	ASN B:20 , HIS B:25 , LEU B:97 , TYR B:147 , LYS B:193 , ASN B:223 , HIS B:320 , SER B:321 , ASN B:322 , HIS B:349 , ARG B:404 , HOH B:601 , HOH B:689 , HOH B:690	BINDING SITE FOR RESIDUE TLA B 501
4	AC4	SOFTWARE	ASP B:221 , ASN B:223 , GLU B:246 , ASP B:247 , ASN B:269 , HOH B:689	BINDING SITE FOR RESIDUE K B 502
5	AC5	SOFTWARE	ASN C:20 , HIS C:25 , LEU C:97 , PHE C:149 , LYS C:193 , ASN C:223 , HIS C:320 , ASN C:322 , HIS C:349 , ARG C:404 , HOH C:601 , HOH C:645 , HOH C:749	BINDING SITE FOR RESIDUE TLA C 501
6	AC6	SOFTWARE	ASP C:221 , ASN C:223 , GLU C:246 , ASP C:247 , ASN C:269 , HOH C:749	BINDING SITE FOR RESIDUE K C 502
7	AC7	SOFTWARE	ASP D:221 , GLU D:246 , ASN D:269 , HOH D:602 , HOH D:603 , HOH D:607	BINDING SITE FOR RESIDUE MG D 501
8	AC8	SOFTWARE	ASN D:20 , HIS D:25 , PRO D:99 , LYS D:193 , ASN D:223 , HIS D:349 , ARG D:404 , HOH D:603 , HOH D:604 , HOH D:605 , HOH D:608 , HOH D:819	BINDING SITE FOR RESIDUE TLA D 502
9	AC9	SOFTWARE	ARG C:301 , HOH C:760 , ARG D:301 , GLN D:304 , HOH D:732	BINDING SITE FOR RESIDUE BCT D 503

(no "SS Bond" information available for 4IT1)

Asymmetric Unit

No.	Residues
1	Lys A:421	-	Pro A:422
2	Lys B:88	-	Pro B:89
3	Lys B:421	-	Pro B:422
4	Lys C:421	-	Pro C:422
5	Lys D:421	-	Pro D:422

(no "SAP(SNP)/Variant" information available for 4IT1)

(no "PROSITE Motif" information available for 4IT1)

(no "Exon" information available for 4IT1)

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:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4it1a1 A:-1-135 automated matches                                                                                                       d4it1a2 A:136-424 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeee.............eeeeeeeeeee....eeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....eee..eee.....................hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh....eee....hhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh.........hhhhh.................eee...........hhhhhhhhhhhhhhhh....hhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4it1 A  -1 QSMKITRVTVTPIAFRDPPLLNASGIHEPFALRSIIEIESDNGYIGLGESYGDAPALAIQQQVQSQLIGLDPFNLNQLRRIVQTTVAAHKPASLAGAELAPGSHASKAVSNAYSAFEVAFLDLQARYLNVPLVDLLGGAVRDEVPFSAYLFFKYAQHVDSPYKPDNWGEALNEQQIVAQAARMIEAYGFKSIKLKAGTLPPEHEVACIKALKKAFPGYPLRIDPNGNWSLETSIRMAELLGDDLQYYEDPTPGLEGMAELHKRTGLPLATNMVVTDFDEFRRSVAQNSVQIVLADHHYWGGLRDTQTLAKMCDTFGLGVSMHSNSHLGISLMAMAHVAAAVPNLDYACDTHYPWQEPDEEVIKGGKLPIVDGCVKITRAPGLGLELDHDQLGKLHDQYLTCGIRQRDDVRQMQRYKPDWKALKPRF 424
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418

Chain B from PDB  Type:PROTEIN  Length:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4it1b1 B:0-135 automated matches                                                                                                       d4it1b2 B:136-424 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.............eeeeeeeeeee....eeeeee..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.....eee..eee.....................hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh....eee....hhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh...........hhhhhhhhhh............eee...........hhhhhhhhhhhhhhhh....hhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4it1 B   0 SMKITRVTVTPIAFRDPPLLNASGIHEPFALRSIIEIESDNGYIGLGESYGDAPALAIQQQVQSQLIGLDPFNLNQLRRIVQTTVAAHKPASLAGAELAPGSHASKAVSNAYSAFEVAFLDLQARYLNVPLVDLLGGAVRDEVPFSAYLFFKYAQHVDSPYKPDNWGEALNEQQIVAQAARMIEAYGFKSIKLKAGTLPPEHEVACIKALKKAFPGYPLRIDPNGNWSLETSIRMAELLGDDLQYYEDPTPGLEGMAELHKRTGLPLATNMVVTDFDEFRRSVAQNSVQIVLADHHYWGGLRDTQTLAKMCDTFGLGVSMHSNSHLGISLMAMAHVAAAVPNLDYACDTHYPWQEPDEEVIKGGKLPIVDGCVKITRAPGLGLELDHDQLGKLHDQYLTCGIRQRDDVRQMQRYKPDWKALKPRF 424
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419

Chain C from PDB  Type:PROTEIN  Length:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4it1c1 C:-1-135 automated matches                                                                                                       d4it1c2 C:136-424 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeee.............eeeeeeeeeee....eeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....eee..eee.....................hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh....eee....hhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh.........hhhhhhhhhh............eee...........hhhhhhhhhhhhhhh.....hhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4it1 C  -1 QSMKITRVTVTPIAFRDPPLLNASGIHEPFALRSIIEIESDNGYIGLGESYGDAPALAIQQQVQSQLIGLDPFNLNQLRRIVQTTVAAHKPASLAGAELAPGSHASKAVSNAYSAFEVAFLDLQARYLNVPLVDLLGGAVRDEVPFSAYLFFKYAQHVDSPYKPDNWGEALNEQQIVAQAARMIEAYGFKSIKLKAGTLPPEHEVACIKALKKAFPGYPLRIDPNGNWSLETSIRMAELLGDDLQYYEDPTPGLEGMAELHKRTGLPLATNMVVTDFDEFRRSVAQNSVQIVLADHHYWGGLRDTQTLAKMCDTFGLGVSMHSNSHLGISLMAMAHVAAAVPNLDYACDTHYPWQEPDEEVIKGGKLPIVDGCVKITRAPGLGLELDHDQLGKLHDQYLTCGIRQRDDVRQMQRYKPDWKALKPRF 424
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418

Chain D from PDB  Type:PROTEIN  Length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4it1d1 D:-2-135 automated matches                                                                                                        d4it1d2 D:136-424 automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....eee..eeee....................hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh....eee...hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh.........hhhhh.................eee...........hhhhhhhhhhhhhhhh....hhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4it1 D  -2 FQSMKITRVTVTPIAFRDPPLLNASGIHEPFALRSIIEIESDNGYIGLGESYGDAPALAIQQQVQSQLIGLDPFNLNQLRRIVQTTVAAHKPASLAGAELAPGSHASKAVSNAYSAFEVAFLDLQARYLNVPLVDLLGGAVRDEVPFSAYLFFKYAQHVDSPYKPDNWGEALNEQQIVAQAARMIEAYGFKSIKLKAGTLPPEHEVACIKALKKAFPGYPLRIDPNGNWSLETSIRMAELLGDDLQYYEDPTPGLEGMAELHKRTGLPLATNMVVTDFDEFRRSVAQNSVQIVLADHHYWGGLRDTQTLAKMCDTFGLGVSMHSNSHLGISLMAMAHVAAAVPNLDYACDTHYPWQEPDEEVIKGGKLPIVDGCVKITRAPGLGLELDHDQLGKLHDQYLTCGIRQRDDVRQMQRYKPDWKALKPRF 424
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417

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: Enolase N-terminal domain-like (211)

Superfamily: Enolase N-terminal domain-like (211)

Family: automated matches (123)

Protein domain: automated matches (123)

Pseudomonas fluorescens [TaxId: 205922] (1)

1a	d4it1a1	A:-1-135
1b	d4it1b1	B:0-135
1c	d4it1c1	C:-1-135
1d	d4it1d1	D:-2-135

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Enolase C-terminal domain-like (212)

Family: automated matches (102)

Protein domain: automated matches (102)

Pseudomonas fluorescens [TaxId: 205922] (1)

2a	d4it1a2	A:136-424
2b	d4it1b2	B:136-424
2c	d4it1c2	C:136-424
2d	d4it1d2	D:136-424

(no "CATH Domain" information available for 4IT1)

(no "Pfam Domain" information available for 4IT1)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:421 - Pro A:422	[ RasMol ]
		Lys B:421 - Pro B:422	[ RasMol ]
		Lys B:88 - Pro B:89	[ RasMol ]
		Lys C:421 - Pro C:422	[ RasMol ]
		Lys D:421 - Pro D:422	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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