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Title :   HIGH RESOLUTION STRUCTURE OF BOVINE ALPHA-CHYMOTRYPSIN

Authors :   A. Razeto, B. Galunsky, V. Kasche, K. S. Wilson, V. S. Lamzin

Date :   31 Jan 05 (Deposition) - 14 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.34

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Serine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Razeto, B. Galunsky, V. Kasche, K. S. Wilson, V. S. Lamzin
High Resolution Structure Of Native Bovine Alpha-Chymotrypsin
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CHYMOTRYPSIN A, CHAIN A
	Chains	:	A, B
	EC Number	:	3.4.21.1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	ALPHA-CHYMOTRYPSIN, CHYMOTRYPSINOGEN A

Molecule 2 - CHYMOTRYPSIN A, CHAIN B
	Chains	:	C, D
	EC Number	:	3.4.21.1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	ALPHA-CHYMOTRYPSIN, CHYMOTRYPSINOGEN A

Molecule 3 - CHYMOTRYPSIN A, CHAIN C
	Chains	:	E, F
	EC Number	:	3.4.21.1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	ALPHA-CHYMOTRYPSIN, CHYMOTRYPSINOGEN A

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP E:172 , SER E:218 , HOH E:1337 , HOH E:1348 , LYS F:175 , SO4 F:1301	BINDING SITE FOR RESIDUE SO4 E 1300
2	AC2	SOFTWARE	LYS E:175 , SO4 E:1300 , HOH E:1406 , TYR F:171 , TRP F:172 , SER F:217 , SER F:218 , HOH F:1352	BINDING SITE FOR RESIDUE SO4 F 1301
3	AC3	SOFTWARE	LYS C:90 , SER C:96 , HOH C:1355 , ARG D:145 , HOH D:2355	BINDING SITE FOR RESIDUE SO4 D 1302
4	AC4	SOFTWARE	LYS C:90 , ASN C:91 , SER C:92 , HOH C:1344 , HOH C:1467 , TRP E:237 , HOH E:1378	BINDING SITE FOR RESIDUE SO4 C 1303
5	AC5	SOFTWARE	ASN D:91 , SER D:92 , HOH D:2328 , HOH D:2370 , HOH D:2377 , TRP F:237	BINDING SITE FOR RESIDUE SO4 D 2300

Asymmetric/Biological Unit

No.	Residues
1	A:1	-	C:122
2	B:1	-	D:122
3	C:42	-	C:58
4	C:136	-	E:201
5	D:42	-	D:58
6	D:136	-	F:201
7	E:168	-	E:182
8	E:191	-	E:220
9	F:168	-	F:182
10	F:191	-	F:220

(no "Cis Peptide Bond" information available for 1YPH)

(no "SAP(SNP)/Variant" information available for 1YPH)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	CTRA_BOVIN	16-243	2	C:16-146 D:16-146
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CTRA_BOVIN	53-58	2	C:53-58 D:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CTRA_BOVIN	189-200	2	E:189-200 F:189-200

(no "Exon" information available for 1YPH)

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:10
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:10
                                    10
           CTRA_BOVIN     1 CGVPAIQPVL  10
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                PROSITE (1) ---------- PROSITE (1)
                PROSITE (2) ---------- PROSITE (2)
                 Transcript ---------- Transcript
                 1yph A   1 CGVPAIQPVL  10
                                    10

Chain B from PDB  Type:PROTEIN  Length:12
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:12
                                    10  
           CTRA_BOVIN     1 CGVPAIQPVLSG  12
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                PROSITE (1) ------------ PROSITE (1)
                PROSITE (2) ------------ PROSITE (2)
                 Transcript ------------ Transcript
                 1yph B   1 CGVPAIQPVLSG  12
                                    10

Chain C from PDB  Type:PROTEIN  Length:131
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:131
                                    25        35        45        55        65        75        85        95       105       115       125       135       145 
           CTRA_BOVIN    16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRY 146
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yphC00 C:16-146 Trypsin-like serine proteases                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeeee..eeeehhhhh.....eeee............eeeeeeeeee.............eeeee..........................eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: C:16-146 UniProt: 16-243                                                                                          PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yph C  16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRY 146
                                    25        35        45        55        65        75        85        95       105       115       125       135       145

Chain D from PDB  Type:PROTEIN  Length:131
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:131
                                    25        35        45        55        65        75        85        95       105       115       125       135       145 
           CTRA_BOVIN    16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRY 146
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yphD00 D:16-146 Trypsin-like serine proteases                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeeee..eeeehhhhh.....eeee............eeeeeeeeee.............eeeee..........................eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: D:16-146 UniProt: 16-243                                                                                          PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yph D  16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRY 146
                                    25        35        45        55        65        75        85        95       105       115       125       135       145

Chain E from PDB  Type:PROTEIN  Length:97
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:97
                                   158       168       178       188       198       208       218       228       238       
           CTRA_BOVIN   149 ANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yphE00 E:149-245 Trypsin-like serine proteases                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhh...eeeee.............eeeeee..eeeeeeeeee.........eeeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: - UniProt: 16-243                                                            -- PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1yph E 149 ANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
                                   158       168       178       188       198       208       218       228       238

Chain F from PDB  Type:PROTEIN  Length:97
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:97
                                   158       168       178       188       198       208       218       228       238       
           CTRA_BOVIN   149 ANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yphF00 F:149-245 Trypsin-like serine proteases                                                   CATH domains
           Pfam domains (1) Trypsin-1yphF01 F:149-238                                                                 ------- Pfam domains (1)
           Pfam domains (2) Trypsin-1yphF02 F:149-238                                                                 ------- Pfam domains (2)
           Pfam domains (3) Trypsin-1yphF03 F:149-238                                                                 ------- Pfam domains (3)
           Pfam domains (4) Trypsin-1yphF04 F:149-238                                                                 ------- Pfam domains (4)
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhh...eeeee.............eeeeee..eeeeeeeeee.........eeeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: - UniProt: 16-243                                                            -- PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1yph F 149 ANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
                                   158       168       178       188       198       208       218       228       238

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 1YPH)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Cattle (Bos taurus) (308)

1a	1yphE00	E:149-245
1b	1yphF00	F:149-245
1c	1yphC00	C:16-146
1d	1yphD00	D:16-146

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Bos taurus (Bovine) (190)

1a	Trypsin-1yphF01	F:149-238
1b	Trypsin-1yphF02	F:149-238
1c	Trypsin-1yphF03	F:149-238
1d	Trypsin-1yphF04	F:149-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (CTRA_BOVIN | P00766)

molecular function
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric/Biological Unit
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4cha	STRUCTURE OF ALPHA-CHYMOTRYPSIN REFINED AT 1.68 A RESOLUTION.
5cha	THE REFINEMENT AND THE STRUCTURE OF THE DIMER OF ALPHA- CHYMOTRYPSIN AT 1.67-A RESOLUTION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (10, 10)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

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Gene Ontology (9, 9)

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