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Title :   X-RAY ANALYSES OF ASPARTIC PROTEINASES IV. STRUCTURE AND REFINEMENT AT 2.2 ANGSTROMS RESOLUTION OF BOVINE CHYMOSIN

Authors :   M. Newman, C. Frazao, G. Khan, I. J. Tickle, T. L. Blundell, M. Safro, N. Andreeva, A. Zdanov

Date :   01 Nov 91 (Deposition) - 07 Nov 91 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase (Acid Proteinase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Newman, M. Safro, C. Frazao, G. Khan, A. Zdanov, I. J. Tickle, T. L. Blundell, N. Andreeva
X-Ray Analyses Of Aspartic Proteinases. Iv. Structure And Refinement At 2. 2 A Resolution Of Bovine Chymosin.
J. Mol. Biol. V. 221 1295 1991
PubMed-ID: 1942052
(for further references see the PDB file header)

Molecule 1 - CHYMOSIN B
	Chains	:	A
	EC Number	:	3.4.23.4
	Engineered	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4CMS)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	AUTHOR	ASP A:32	ACTIVE SITE
2	AC2	AUTHOR	ASP A:215	ACTIVE SITE

Asymmetric/Biological Unit

No.	Residues
1	A:45	-	A:50
2	A:206	-	A:210
3	A:249	-	A:282

Asymmetric/Biological Unit

No.	Residues
1	Thr A:22	-	Pro A:23

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CHYM_BOVIN_001 *	G	302	D	CHYM_BOVIN	---	---	A	G	243	D
	* ID not provided by source

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

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	CHYM_BOVIN	74-378	1	A:14-323
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CHYM_BOVIN	89-100 271-282	2	A:29-40 A:212-223

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000013970	1	ENSBTAE00000266971	chr3:35631399-35631313	87	CHYM_BOVIN	1-21	21	0	-	-
1.2	ENSBTAT00000013970	2	ENSBTAE00000266969	chr3:35628381-35628231	151	CHYM_BOVIN	21-71	51	1	A:-2-11	13
1.3	ENSBTAT00000013970	3	ENSBTAE00000114008	chr3:35627470-35627353	118	CHYM_BOVIN	72-111	40	1	A:12-51	40
1.4	ENSBTAT00000013970	4	ENSBTAE00000114011	chr3:35626285-35626167	119	CHYM_BOVIN	111-150	40	1	A:51-90	40
1.5	ENSBTAT00000013970	5	ENSBTAE00000266967	chr3:35624649-35624450	200	CHYM_BOVIN	151-217	67	1	A:91-157	67
1.6	ENSBTAT00000013970	6	ENSBTAE00000114017	chr3:35623869-35623756	114	CHYM_BOVIN	217-255	39	1	A:157-196 (gaps)	40
1.7	ENSBTAT00000013970	7	ENSBTAE00000114020	chr3:35622433-35622289	145	CHYM_BOVIN	255-303	49	1	A:196-244	49
1.8	ENSBTAT00000013970	8	ENSBTAE00000114021	chr3:35621673-35621575	99	CHYM_BOVIN	304-336	33	1	A:245-277	33
1.9	ENSBTAT00000013970	9	ENSBTAE00000266965	chr3:35620863-35620595	269	CHYM_BOVIN	337-381	45	1	A:278-326 (gaps)	49

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:320
 aligned with CHYM_BOVIN | P00794 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:323
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378   
           CHYM_BOVIN    59 GEVASVPLTNYLDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNACKNHQRFDPRKSSTFQNLGKPLSIHYGTGSMQGILGYDTVTVSNIVDIQQTVGLSTQEPGDVFTYAEFDGILGMAYPSLASEYSIPVFDNMMNRHLVAQDLFSVYMDRNGQESMLTLGAIDPSYYTGSLHWVPVTVQQYWQFTVDSVTISGVVVACEGGCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQSENHSQKWILGDVFIREYYSVFDRANNLVGLAKAI 381
               SCOP domains d4cmsa_ A: Chymosin (synonym: renin)                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --4cmsA01 A:1-170 Acid Proteases                                                                                                                                           4cmsA02 A:171-325 Acid Proteases                                                                                                                       - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.eee...eeeeeeee....eeeeeeee.....eeee......hhhh......hhh....ee...eeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeee...hhhhh....eeee...hhh.......hhhhhhh.......eeeee........eeee....hhheeeeeeeee......eeeeeeeeee..eeee....eeeee......eeeehhhhhhhhhhh..ee.....eee...hhhh...eeeee..eeeee.hhhheeee..eeee.eeee---..eee.hhhh..eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PEPTIDASE_A1  PDB: A:14-323 UniProt: 74-378                                                                                                                                                                                                                                                                      --- PROSITE (1)
                PROSITE (2) ------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2     Exon 1.3  PDB: A:12-51 UniProt: 72-111  ---------------------------------------Exon 1.5  PDB: A:91-157 UniProt: 151-217                           -------------------------------------Exon 1.7  PDB: A:196-244 UniProt: 255-303        Exon 1.8  PDB: A:245-277         Exon 1.9  PDB: A:278-326 (gaps)               Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.4  PDB: A:51-90 UniProt: 111-150 ------------------------------------------------------------------Exon 1.6  PDB: A:157-196 (gaps)        ------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 4cms A  -2 GEVASVPLTNYLDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNACKNHQRFDPRKSSTFQNLGKPLSIHYGTGSMQGILGYDTVTVSNIVDIQQTVGLSTQEPGDVFTYAEFDGILGMAYPSLASEYSIPVFDNMMNRHLVAQDLFSVYMDRNGQESMLTLGAIDPSYYTGSLHWVPVTVQQYWQFTVDSVTISGVVVACEGGCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQSE---QKWILGDVFIREYYSVFDRANNLVGLAKAI 326
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158||     169       179       189       199       209       219       229       239       249       259       269       279       289   |   303       313       323   
                             ||                                                                                                                                                           159|                                                                                                                             289 297                             
                            -1|                                                                                                                                                            161                                                                                                                                                                 
                              1

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: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: Chymosin (synonym: renin) (67)

Cow (Bos taurus) [TaxId: 9913] (6)

d4cmsa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Cathepsin D, subunit A; domain 1 (745)

Homologous Superfamily: Acid Proteases (745)

Cattle (Bos taurus) (4)

1a	4cmsA02	A:171-325
1b	4cmsA01	A:1-170

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CHYM_BOVIN | P00794)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues 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:0007586	digestion	The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Thr A:22 - Pro A:23	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (2, 2)

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (8, 8)

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