3IUT - JenaLib

Title :   THE CRYSTAL STRUCTURE OF CRUZAIN IN COMPLEX WITH A TETRAFLUOROPHENOXYMETHYL KETONE INHIBITOR

Authors :   I. D. Kerr, M. Debnath, L. S. Brinen

Date :   31 Aug 09 (Deposition) - 02 Mar 10 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A

Keywords :   Mature Domain, Papain Family Cysteine Protease, Autocatalytic Cleavage, Disulfide Bond, Glycoprotein, Hydrolase, Protease, Thiol Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Brak, I. D. Kerr, K. T. Barrett, N. Fuchi, M. Debnath, K. Ang, J. C. Engel, J. H. Mckerrow, P. S. Doyle, L. S. Brinen, J. A. Ellman
Nonpeptidic Tetrafluorophenoxymethyl Ketone Cruzain Inhibitors As Promising New Leads For Chagas Disease Chemotherapy.
J. Med. Chem. V. 53 1763 2010
PubMed-ID: 20088534 | Reference-DOI: 10.1021/JM901633V

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:19 , GLY A:23 , SER A:24 , CYS A:25 , TRP A:26 , SER A:61 , SER A:64 , GLY A:65 , GLY A:66 , LEU A:67 , ASP A:161 , HIS A:162 , GLY A:163 , HOH A:265	BINDING SITE FOR RESIDUE KB2 A 300
2	AC2	SOFTWARE	THR A:103 , SER A:104 , GLY A:105 , HIS A:106 , GLY A:149 , VAL A:151 , HOH A:228	BINDING SITE FOR RESIDUE EDO A 222
3	AC3	SOFTWARE	THR A:14 , TYR A:193 , HOH A:304	BINDING SITE FOR RESIDUE EDO A 223
4	AC4	SOFTWARE	CYS A:101 , THR A:102 , THR A:103 , SER A:104 , THR A:146 , HOH A:243 , HOH A:246	BINDING SITE FOR RESIDUE EDO A 224
5	AC5	SOFTWARE	ASP A:18 , GLY A:20 , TRP A:184	BINDING SITE FOR RESIDUE EDO A 225

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 7)

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYSP_TRYCR_009 *	S	146	G	CYSP_TRYCR	---	---	A	S	24	G
2	UniProt	VAR_CYSP_TRYCR_010 *	S	186	G	CYSP_TRYCR	---	---	A	S	64	G
3	UniProt	VAR_CYSP_TRYCR_011 *	A	204	G	CYSP_TRYCR	---	---	A	A	82	G
4	UniProt	VAR_CYSP_TRYCR_012 *	V	286	F	CYSP_TRYCR	---	---	A	V	164	F
5	UniProt	VAR_CYSP_TRYCR_013 *	V	286	L	CYSP_TRYCR	---	---	A	V	164	L
6	UniProt	VAR_CYSP_TRYCR_014 *	T	308	A	CYSP_TRYCR	---	---	A	T	186	A
7	UniProt	VAR_CYSP_TRYCR_015 *	E	313	D	CYSP_TRYCR	---	---	A	E	191	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:215
 aligned with CYSP_TRYCR | P25779 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:215
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     
           CYSP_TRYCR   123 APAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 337
               SCOP domains d3iuta_ A: Cruzain                                                                                                                                                                                                      SCOP domains
               CATH domains 3iutA00 A:1-215 Cysteine proteinases                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhh............hhhhhhhhhhhhhhhhhh.......hhhhhhhhh...hhhhh.hhhhhhhhhhhhh..eee.......................eeee..eeee...hhhhhhhhhhhhh.eeeee...........ee.........eeeeeeeee......eeeee...........eeeee...hhhhh...eeeee.. Sec.struct. author
             SAPs(SNPs) (1) -----------------------G---------------------------------------G-----------------G---------------------------------------------------------------------------------F---------------------A----D------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------L--------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iut A   1 APAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLAEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDGAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CYSP_TRYCR | P25779)

molecular function
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	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: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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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