3FES - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ATP-DEPENDENT CLP PROTEASE CLPC FROM CLOSTRIDIUM DIFFICILE

Authors :   Y. Kim, C. Tesar, H. Li, G. Cobb, A. Joachimiak, Midwest Center For St Genomics (Mcsg)

Date :   01 Dec 08 (Deposition) - 16 Dec 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

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

Keywords :   Alpha-Helical Bundles, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Atp- Binding, Chaperone, Nucleotide-Binding, Protease, Atp Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, C. Tesar, H. Li, G. Cobb, A. Joachimiak
Crystal Structure Of The Atp-Dependent Clp Protease Clpc From Clostridium Difficile
To Be Published
PubMed: search

Molecule 1 - ATP-DEPENDENT CLP ENDOPEPTIDASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-143, ATP-BINDING
	Gene	:	CD0026, CLPC, MECB
	Organism Scientific	:	CLOSTRIDIUM DIFFICILE
	Organism Taxid	:	272563
	Strain	:	630
	Synonym	:	ATP-DEPENDENT CLP PROTEASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 25)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
4	PG4	4	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 3 (3, 7)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:6 , GLY A:103 , THR A:104 , HOH A:163	BINDING SITE FOR RESIDUE MG A 143
2	AC2	SOFTWARE	HIS A:25 , GLU A:67 , GLY A:68 , LYS A:69 , LEU B:23 , LYS B:69 , GLU B:72	BINDING SITE FOR RESIDUE PG4 B 143
3	AC3	SOFTWARE	THR B:6 , GLY B:103 , THR B:104 , HOH B:169 , HOH B:175	BINDING SITE FOR RESIDUE MG B 144
4	AC4	SOFTWARE	HIS C:25 , ILE C:27 , GLY C:29 , SER C:30 , GLU C:31 , GLU C:67 , SER C:80 , ARG C:82 , GLY C:117 , ILE C:118 , ASP D:65 , MSE D:66 , GLU D:67 , LYS D:69	BINDING SITE FOR RESIDUE EPE C 143
5	AC5	SOFTWARE	ARG B:131 , LEU C:136 , ASP C:139 , MSE C:141 , GLY C:142 , HOH C:169	BINDING SITE FOR RESIDUE PG4 C 144
6	AC6	SOFTWARE	MSE C:92 , LYS C:96 , GLN C:113	BINDING SITE FOR RESIDUE PG4 C 145
7	AC7	SOFTWARE	THR C:6 , ARG C:8 , GLY C:103 , THR C:104 , HOH C:147 , HOH C:164	BINDING SITE FOR RESIDUE MG C 146
8	AC8	SOFTWARE	LEU A:97 , THR A:137 , MSE D:92 , LYS D:96 , HOH D:248	BINDING SITE FOR RESIDUE PG4 D 143
9	AC9	SOFTWARE	THR D:6 , GLY D:103 , THR D:104 , HOH D:153	BINDING SITE FOR RESIDUE MG D 144

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

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

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

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

(no "Exon" information available for 3FES)

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:142
 aligned with Q18CA9_PEPD6 | Q18CA9 from UniProtKB/TrEMBL  Length:815

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
         Q18CA9_PEPD6     2 NFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDMEGKGEEISEDIVLSPRSKQILELSGMFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDMMG 143
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fesA00 A:1-142 Double Clp-N motif                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fes A   1 NFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDmEGKGEEISEDIVLSPRSKQILELSGmFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDmmG 142
                                    10        20        30        40        50        60     |  70        80        90 |     100       110       120       130       140| 
                                                                                            66-MSE                    92-MSE                                         140-MSE
                                                                                                                                                                      141-MSE

Chain B from PDB  Type:PROTEIN  Length:141
 aligned with Q18CA9_PEPD6 | Q18CA9 from UniProtKB/TrEMBL  Length:815

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
         Q18CA9_PEPD6     2 NFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDMEGKGEEISEDIVLSPRSKQILELSGMFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDMM 142
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fesB00 B:1-139 Double Clp-N motif                                                                                                         -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fes B   1 NFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDmEGKGEEISEDIVLSPRSKQILELSGmFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDmm 141
                                    10        20        30        40        50        60     |  70        80        90 |     100       110       120       130       140|
                                                                                            66-MSE                    92-MSE                                         140-MSE
                                                                                                                                                                      141-MSE

Chain C from PDB  Type:PROTEIN  Length:140
 aligned with Q18CA9_PEPD6 | Q18CA9 from UniProtKB/TrEMBL  Length:815

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
         Q18CA9_PEPD6     2 NFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDMEGKGEEISEDIVLSPRSKQILELSGMFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDMMG 143
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fesC00 C:1-142 Double Clp-N motif                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhh.....--..eehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fes C   1 NFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDmEGKGEEI--DIVLSPRSKQILELSGmFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDmmG 142
                                    10        20        30        40        50        60     |  70  |  |  80        90 |     100       110       120       130       140| 
                                                                                            66-MSE 73 76              92-MSE                                         140-MSE
                                                                                                                                                                      141-MSE

Chain D from PDB  Type:PROTEIN  Length:142
 aligned with Q18CA9_PEPD6 | Q18CA9 from UniProtKB/TrEMBL  Length:815

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
         Q18CA9_PEPD6     2 NFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDMEGKGEEISEDIVLSPRSKQILELSGMFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDMMG 143
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fesD00 D:1-142 Double Clp-N motif                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fes D   1 NFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDmEGKGEEISEDIVLSPRSKQILELSGmFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDmmG 142
                                    10        20        30        40        50        60     |  70        80        90 |     100       110       120       130       140| 
                                                                                            66-MSE                    92-MSE                                         140-MSE
                                                                                                                                                                      141-MSE

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3FES)

Asymmetric Unit

Classes(

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Double Clp-N motif (16)

Homologous Superfamily: Double Clp-N motif (16)

Clostridium difficile 630. Organism_taxid: 272563. Strain: 630. (1)

1a	3fesA00	A:1-142
1b	3fesD00	D:1-142
1c	3fesB00	B:1-139
1d	3fesC00	C:1-142

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q18CA9_PEPD6 | Q18CA9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0019538	protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.

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Ligands, Modified Residues, Ions (4, 25)

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