4K1F - JenaLib

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Title :   CRYSTAL STRUCTURE OF REDUCED TRYPAREDOXIN PEROXIDASE FROM LEISHMANIA MAJOR AT 2.34 A RESOLUTION

Authors :   A. Ilari, A. Fiorillo, F. Di Chiaro

Date :   05 Apr 13 (Deposition) - 09 Apr 14 (Release) - 10 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.34

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

Keywords :   Thioredoxin Fold, Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Brindisi, S. Brogi, N. Relitti, A. Vallone, S. Butini, S. Gemma, E. Novellino, G. Colotti, G. Angiulli, F. Di Chiaro, A. Fiorillo, A. Ilari, G. Campiani
Structure-Based Discovery Of The First Non-Covalent Inhibitors Of Leishmania Major Tryparedoxin Peroxidase By High Throughput Docking
Sci Rep V. 5 9705 2015
PubMed-ID: 25951439 | Reference-DOI: 10.1038/SREP09705

Molecule 1 - TRYPAREDOXIN PEROXIDASE
	Chains	:	A, B, C, D, E
	EC Number	:	1.11.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TRYP3
	Organism Scientific	:	LEISHMANIA MAJOR
	Organism Taxid	:	5664

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	PE8	1	Ligand/Ion	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
3	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PE8	2	Ligand/Ion	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
3	PEG	8	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:82 , GLN A:123 , MET A:147	BINDING SITE FOR RESIDUE PGE A 201
2	AC2	SOFTWARE	LYS A:168 , HIS A:169	BINDING SITE FOR RESIDUE CL A 202
3	AC3	SOFTWARE	PHE B:165 , HIS B:169 , GLY B:180 , PRO B:182 , GLY B:194 , TYR B:195 , GLN B:199 , HOH B:487 , HOH B:488	BINDING SITE FOR RESIDUE PE8 B 301
4	AC4	SOFTWARE	MET C:147	BINDING SITE FOR RESIDUE PEG C 201
5	AC5	SOFTWARE	LYS C:168 , HIS C:169 , LYS C:179	BINDING SITE FOR RESIDUE CL C 202
6	AC6	SOFTWARE	TYR D:82 , MET E:147	BINDING SITE FOR RESIDUE PEG D 201
7	AC7	SOFTWARE	LYS D:168 , HIS D:169	BINDING SITE FOR RESIDUE CL D 202
8	AC8	SOFTWARE	TYR E:82	BINDING SITE FOR RESIDUE PEG E 201

(no "SS Bond" information available for 4K1F)

(no "Cis Peptide Bond" information available for 4K1F)

(no "SAP(SNP)/Variant" information available for 4K1F)

(no "PROSITE Motif" information available for 4K1F)

(no "Exon" information available for 4K1F)

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:198
                                                                                                                                                                                                                                      
               SCOP domains d4k1fa_ A: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k1f A   2 SCGNAKINSPAPSFEEVALMPNGSFKKISLSSYKGKWVVLFFYPLDFTFVCPTEVIAFSDSVSRFNELNCEVLACSIDSEYAHLQWTLQDRKKGGLGTMAIPILADKTKNIARSYGVLEESQGVAYRGLFIIDPHGMLRQITVNDMPVGRSVEEVLRLLEAFQFVEKHGEVCPANWKKGDPGMKPEPNASVEGYFSKQ 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4k1fb_ B: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh........eee...hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k1f B   2 SCGNAKINSPAPSFEEVALMPNGSFKKISLSSYKGKWVVLFFYPLDFTFVCPTEVIAFSDSVSRFNELNCEVLACSIDSEYAHLQWTLQDRKKGGLGTMAIPILADKTKNIARSYGVLEESQGVAYRGLFIIDPHGMLRQITVNDMPVGRSVEEVLRLLEAFQFVEKHGEVCPANWKKGDPGMKPEPNASVEGYFSKQ 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4k1fc_ C: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh................hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k1f C   2 SCGNAKINSPAPSFEEVALMPNGSFKKISLSSYKGKWVVLFFYPLDFTFVCPTEVIAFSDSVSRFNELNCEVLACSIDSEYAHLQWTLQDRKKGGLGTMAIPILADKTKNIARSYGVLEESQGVAYRGLFIIDPHGMLRQITVNDMPVGRSVEEVLRLLEAFQFVEKHGEVCPANWKKGDPGMKPEPNASVEGYFSKQ 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain D from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains d4k1fd_ D: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh................hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1f D   3 CGNAKINSPAPSFEEVALMPNGSFKKISLSSYKGKWVVLFFYPLDFTFVCPTEVIAFSDSVSRFNELNCEVLACSIDSEYAHLQWTLQDRKKGGLGTMAIPILADKTKNIARSYGVLEESQGVAYRGLFIIDPHGMLRQITVNDMPVGRSVEEVLRLLEAFQFVEKHGEVCPANWKKGDPGMKPEPNASVEGYFSK 198
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain E from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains d4k1fe_ E: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh................hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k1f E   2 SCGNAKINSPAPSFEEVALMPNGSFKKISLSSYKGKWVVLFFYPLDFTFVCPTEVIAFSDSVSRFNELNCEVLACSIDSEYAHLQWTLQDRKKGGLGTMAIPILADKTKNIARSYGVLEESQGVAYRGLFIIDPHGMLRQITVNDMPVGRSVEEVLRLLEAFQFVEKHGEVCPANWKKGDPGMKPEPNASVEGYFSK 198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Glutathione peroxidase-like (136)

Protein domain: automated matches (46)

Leishmania major [TaxId: 5664] (2)

1a	d4k1fa_	A:
1b	d4k1fb_	B:
1c	d4k1fc_	C:
1d	d4k1fd_	D:
1e	d4k1fe_	E:

(no "CATH Domain" information available for 4K1F)

(no "Pfam Domain" information available for 4K1F)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4k1f)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 5)

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Gene Ontology (6, 6)

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