2ZPL - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF PDZ DOMAIN A

Authors :   K. Inaba, M. Suzuki

Date :   17 Jul 08 (Deposition) - 21 Oct 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: A,B,C  (1x)

Keywords :   Metalloproteinase, Membrane Protein, Pdz-Domain, Hydrolase, Inner Membrane, Membrane, Metal-Binding, Metalloprotease, Protease, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Inaba, M. Suzuki, K. Maegawa, Y. Akiyama
Crystal Structure Analysis Of Pdz-Domain A
To Be Published
PubMed: search

Molecule 1 - REGULATOR OF SIGMA E PROTEASE
	Chains	:	A, B, C
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ-DOMAIN A
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	NI	3	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:175 , HOH A:222 , HOH A:224 , HOH A:260 , GLY C:125	BINDING SITE FOR RESIDUE NI A 1
2	AC2	SOFTWARE	HIS A:199 , HOH B:4 , HOH B:5 , HOH B:6 , GLY B:125	BINDING SITE FOR RESIDUE NI B 2
3	AC3	SOFTWARE	HOH B:25 , ARG B:128 , HOH C:96 , ILE C:173 , GLY C:174 , ASP C:175 , TRP C:200 , PHE C:202	BINDING SITE FOR RESIDUE GOL C 1
4	AC4	SOFTWARE	HOH B:27 , HOH B:84 , ASP B:161 , TRP B:162 , ASP B:163	BINDING SITE FOR RESIDUE GOL B 222

(no "SS Bond" information available for 2ZPL)

(no "Cis Peptide Bond" information available for 2ZPL)

(no "SAP(SNP)/Variant" information available for 2ZPL)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	RSEP_ECOLI	199-291	3	A:199-218 B:199-218 C:199-218

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	RSEP_ECOLI	199-291	1	A:199-218 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	RSEP_ECOLI	199-291	1	- B:199-218 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	RSEP_ECOLI	199-291	1	- - C:199-218

Biological Unit 4 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	RSEP_ECOLI	199-291	3	A:199-218 B:199-218 C:199-218

(no "Exon" information available for 2ZPL)

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:92
 aligned with RSEP_ECOLI | P0AEH1 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:92
                                   136       146       156       166       176       186       196       206       216  
           RSEP_ECOLI   127 VRPVVGEIAANSIAAEAQIAPGTELKAVDGIETPDWDAVRLQLVDKIGDESTTITVAPFGSDQRRDVKLDLRHWAFEPDKEDPVSSLGIRPR 218
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhh......eeeee..ee..hhhhhhhhhhh.....eeeeeee.......eeeeee...........hhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------PDZ  PDB: A:199-218  PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2zpl A 127 VRPVVGEIAANSIAAEAQIAPGTELKAVDGIETPDWDAVRLQmVDKIGDESTTITVAPFGSDQRRDVKLDLRHWAFEPDKEDPVSSLGIRPR 218
                                   136       146       156       166  |    176       186       196       206       216  
                                                                    169-MSE

Chain B from PDB  Type:PROTEIN  Length:94
 aligned with RSEP_ECOLI | P0AEH1 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:115
                                   113       123       133       143       153       163       173       183       193       203       213     
           RSEP_ECOLI   104 GPVANFIFAIFAYWLVFIIGVPGVRPVVGEIAANSIAAEAQIAPGTELKAVDGIETPDWDAVRLQLVDKIGDESTTITVAPFGSDQRRDVKLDLRHWAFEPDKEDPVSSLGIRPR 218
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---------------------.....eeee...hhhhhh......eeeee..ee..hhhhhhhhhhh.....eeeeeee.......eeeeee...........hhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------PDZ  PDB: B:199-218  PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2zpl B 125 G---------------------SVRPVVGEIAANSIAAEAQIAPGTELKAVDGIETPDWDAVRLQmVDKIGDESTTITVAPFGSDQRRDVKLDLRHWAFEPDKEDPVSSLGIRPR 218
                            |        -         -  |    133       143       153       163     | 173       183       193       203       213     
                          125                   126                                        169-MSE

Chain C from PDB  Type:PROTEIN  Length:89
 aligned with RSEP_ECOLI | P0AEH1 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:115
                                   113       123       133       143       153       163       173       183       193       203       213     
           RSEP_ECOLI   104 GPVANFIFAIFAYWLVFIIGVPGVRPVVGEIAANSIAAEAQIAPGTELKAVDGIETPDWDAVRLQLVDKIGDESTTITVAPFGSDQRRDVKLDLRHWAFEPDKEDPVSSLGIRPR 218
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------PDZ-2zplC01      Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------PDZ-2zplC02      Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------PDZ-2zplC03      Pfam domains (3)
           Pfam domains (4) -                     -Peptidase_M50-2zplC04 C:127-218                                                              Pfam domains (4)
           Pfam domains (5) -                     -Peptidase_M50-2zplC05 C:127-218                                                              Pfam domains (5)
           Pfam domains (6) -                     -Peptidase_M50-2zplC06 C:127-218                                                              Pfam domains (6)
         Sec.struct. author .---------------------.....eeee...hhhhhh......eeeee..ee..hhhhhhhhhhh.....eeeeeee.-----.eeeeee...........hhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------PDZ  PDB: C:199-218  PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2zpl C 125 G---------------------SVRPVVGEIAANSIAAEAQIAPGTELKAVDGIETPDWDAVRLQmVDKIGDESTTITVAP-----RRDVKLDLRHWAFEPDKEDPVSSLGIRPR 218
                            |        -         -  |    133       143       153       163     | 173       183|     |193       203       213     
                          125                   126                                        169-MSE        184   190

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 '\|'

(no "SCOP Domain" information available for 2ZPL)

(no "CATH Domain" information available for 2ZPL)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Escherichia coli (strain K12) (21)

1a	PDZ-2zplC01	C:203-218
1b	PDZ-2zplC02	C:203-218
1c	PDZ-2zplC03	C:203-218

Clan: Peptidase_MA (251)

Family: Peptidase_M50 (2)

Escherichia coli (strain K12) (2)

2a	Peptidase_M50-2zplC04	C:127-218
2b	Peptidase_M50-2zplC05	C:127-218
2c	Peptidase_M50-2zplC06	C:127-218

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RSEP_ECOLI | P0AEH1)

molecular function
	GO:0043856	anti-sigma factor antagonist activity	The function of binding to an anti-sigma factor and stopping, preventing or reducing the rate of its activity.
	GO:0045152	antisigma factor binding	Interacting selectively and non-covalently with an antisigma factor, a factor which inhibits the ability of the sigma factor to function as a transcriptional initiator.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	RSEP_ECOLI \| P0AEH1	:	2zpm 3id1 3id2 3id3 3id4

(no "Related Entries Specified in the PDB File" available for 2ZPL)

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (4, 4)

SS Bonds (0, 0)

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