4TKY - JenaLib

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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 :   THE COMPLEX STRUCTURE OF E. COLI DSBA BOUND TO A PEPTIDE AT THE DSBA/DSBB INTERFACE

Authors :   L. Premkumar, J. L. Martin

Date :   28 May 14 (Deposition) - 14 Jan 15 (Release) - 04 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Dsba, Dsbb, Dithiol Oxidase, Complex, Dsba/Dsbb, Peptide Inhibitor, Thioredoxin-Related Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Duprez, L. Premkumar, M. A. Halili, F. Lindahl, R. C. Reid, D. P. Fairlie, J. L. Martin
Peptide Inhibitors Of The Escherichia Coli Dsba Oxidative Machinery Essential For Bacterial Virulence.
J. Med. Chem. V. 58 577 2015
PubMed-ID: 25470204 | Reference-DOI: 10.1021/JM500955S

Molecule 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 20-208
	Gene	:	DSBA, DSF, PPFA, B3860, JW3832
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

Molecule 2 - PRO-PHE-ALA-THR-CYS-ASP-SER
	Chains	:	F, E, G, H
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A				E
Biological Unit 2 (1x)	:		B				F
Biological Unit 3 (1x)	:			C					H
Biological Unit 4 (1x)	:				D			G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	ACE	4	Mod. Amino Acid	ACETYL GROUP
2	NH2	4	Ligand/Ion	AMINO GROUP

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	1	Ligand/Ion	AMINO GROUP

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	1	Ligand/Ion	AMINO GROUP

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	1	Ligand/Ion	AMINO GROUP

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	1	Ligand/Ion	AMINO GROUP

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:35 , TYR D:34 , GLN D:35 , PHE E:101 , ALA E:102	binding site for Di-peptide ACE E 201 and PRO E 100
2	AC2	SOFTWARE	ARG A:148 , HOH A:237 , ASN C:62 , GLU C:139 , ASP E:105	binding site for Di-peptide NH2 E 202 and SER E 106
3	AC3	SOFTWARE	GLN B:35 , LEU B:40 , PHE B:174 , TYR C:34 , GLN C:35 , PHE F:101 , ALA F:102	binding site for Di-peptide ACE F 201 and PRO F 100
4	AC4	SOFTWARE	ARG B:148 , ASN D:62 , HOH D:201 , HOH D:210 , ASP F:105 , HOH F:301	binding site for Di-peptide NH2 F 202 and SER F 106
5	AC5	SOFTWARE	HOH A:215 , LEU D:40 , PHE D:174 , PHE G:101 , ALA G:102	binding site for Di-peptide ACE G 201 and PRO G 100
6	AC6	SOFTWARE	PHE D:63 , ARG D:148 , ASP G:105	binding site for Di-peptide NH2 G 202 and SER G 106
7	AC7	SOFTWARE	PRO B:31 , GLN B:97 , LEU C:40 , MET C:171 , PHE H:101 , ALA H:102	binding site for Di-peptide ACE H 201 and PRO H 100
8	AC8	SOFTWARE	PHE C:63 , ARG C:148 , HOH C:229 , ASP H:105 , HOH H:304	binding site for Di-peptide NH2 H 202 and SER H 106

Asymmetric Unit

No.	Residues
1	A:30	-	E:104
2	B:30	-	F:104
3	C:30	-	H:104
4	D:30	-	G:104

Asymmetric Unit

No.	Residues
1	Val A:150	-	Pro A:151
2	Val B:150	-	Pro B:151
3	Val C:150	-	Pro C:151
4	Val D:150	-	Pro D:151

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

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

(no "Exon" information available for 4TKY)

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:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..........eeeee...hhhhhhhhhh.hhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeee...eee.hhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tky A   1 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..........eeeee...hhhhhhhhhh.hhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.eeee...eee.hhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tky B   1 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain C from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..........eeeee...hhhhhhhhhh.hhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.eeee...eee.hhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tky C   1 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain D from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..........eeeee...hhhhhhhhhh.hhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.eeee...eee.hhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tky D   1 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain E from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ....ee.. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4tky E 100 PFATCDSx 201
                                  ||
                                106|
                                 201-ACE

Chain F from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ....ee.. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4tky F 100 PFATCDSx 201
                                  ||
                                106|
                                 201-ACE

Chain G from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ....ee.. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4tky G 100 PFATCDSx 201
                                  ||
                                106|
                                 201-ACE

Chain H from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ....ee.. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4tky H 100 PFATCDSx 201
                                  ||
                                106|
                                 201-ACE

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 4TKY)

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

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

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Asymmetric Unit
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		AC7	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Val A:150 - Pro A:151	[ RasMol ]
		Val B:150 - Pro B:151	[ RasMol ]
		Val C:150 - Pro C:151	[ RasMol ]
		Val D:150 - Pro D:151	[ RasMol ]

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	4tky
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(no "Related Entries Specified in the PDB File" available for 4TKY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (8, 8)

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