4MA8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE PRION PROTEIN COMPLEXED WITH CHLORPROMAZINE

Authors :   P. K. Baral, M. Swayampakula, M. N. G. James

Date :   15 Aug 13 (Deposition) - 22 Jan 14 (Release) - 26 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : C,H,L

Keywords :   Immunoglobulin Fold, Fab, Antibody, Mouse Prion Protein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. K. Baral, M. Swayampakula, M. K. Rout, N. N. Kav, L. Spyracopoulos, A. Aguzzi, M. N. James
Structural Basis Of Prion Inhibition By Phenothiazine Compounds.
Structure V. 22 291 2014
PubMed-ID: 24373770 | Reference-DOI: 10.1016/J.STR.2013.11.009

Molecule 1 - MAJOR PRION PROTEIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 116-229
	Gene	:	PRNP, PRN-P, PRP
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	PRP, PRP27-30, PRP33-35C

Molecule 2 - POM1 HEAVY CHAIN
	Cell	:	HYBRIDOMA
	Chains	:	H
	Engineered	:	YES
	Fragment	:	FAB
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - POM1 LIGHT CHAIN
	Cell	:	HYBRIDOMA
	Chains	:	L
	Engineered	:	YES
	Fragment	:	FAB
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3
Asymmetric/Biological Unit	:	C	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	Z80	1	Ligand/Ion	3-(2-CHLORO-10H-PHENOTHIAZIN-10-YL)-N,N-DIMETHYLPROPAN-1-AMINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU C:125 , ILE C:182 , LYS C:185 , GLN C:186	BINDING SITE FOR RESIDUE Z80 C 301

Asymmetric/Biological Unit

No.	Residues
1	C:179	-	C:214
2	H:22	-	H:96
3	H:145	-	H:200
4	L:23	-	L:88
5	L:134	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Gly C:124	-	Leu C:125
2	Leu C:125	-	Gly C:126
3	Phe H:151	-	Pro H:152
4	Glu H:153	-	Pro H:154
5	Trp H:193	-	Pro H:194
6	Ser L:7	-	Pro L:8
7	Trp L:94	-	Pro L:95
8	Tyr L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 4MA8)

(no "PROSITE Motif" information available for 4MA8)

(no "Exon" information available for 4MA8)

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 C from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee............hhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4ma8 C 119 GAVVGGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYY 226
                                   128       138       148       158       168       178       188       198       208       218

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee.........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ma8 H   1 QVQLQQSGTELVMPGASVKMSCKASGYTFTDYWMHWVKQRPGQGLEWIGSIDPSDSYTSHNEKFKGKATLTVDESSSTAYMQLSSLTSEDSAVYFCSRSGYGYYAMEYWGQGTSVTVSSAKTTPPSVYPLAPGGGATNSMVTLGCLVKGYFPEPVTVTWNSGSLSGGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4ma8l1 L:1-107 automated matches                                                                          d4ma8l2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeee....eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ma8 L   1 DIVLTQSPAILSVSPGERVSFSCRASQNIGTSIHWYQQRTNESPRLIIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQSNTWPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSETDQDSKDSTYSMSSTLTLTKDEYERHNTYTCEATHKTSTSPIVKSFNRNE 213
                                    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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

d4ma8l1

L:1-107

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

d4ma8l2

L:108-213

(no "CATH Domain" information available for 4MA8)

(no "Pfam Domain" information available for 4MA8)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		Z80	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu H:153 - Pro H:154	[ RasMol ]
		Gly C:124 - Leu C:125	[ RasMol ]
		Leu C:125 - Gly C:126	[ RasMol ]
		Phe H:151 - Pro H:152	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp H:193 - Pro H:194	[ RasMol ]
		Trp L:94 - Pro L:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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		Orientation in Membranes	:	OPM
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		Interatomic Contacts of Structural Units	:	CSU
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (5, 5)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (40, 40)

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