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Title :   X-RAY CRYSTAL STRUCTURE OF GAMMA-CHYMOTRYPSIN IN HEXANE

Authors :   N. H. Yennawar, H. P. Yennawar, S. Banerjee, G. K. Farber

Date :   20 Aug 93 (Deposition) - 31 Oct 93 (Release) - 24 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : B,E,F,G
Biol. Unit 1: B,E,F,G  (2x)

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

Reference :   N. H. Yennawar, H. P. Yennawar, G. K. Farber
X-Ray Crystal Structure Of Gamma-Chymotrypsin In Hexane.
Biochemistry V. 33 7326 1994
PubMed-ID: 8003497 | Reference-DOI: 10.1021/BI00189A038

Molecule 1 - GAMMA-CHYMOTRYPSIN A
	Chains	:	E
	EC Number	:	3.4.21.1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 2 - GAMMA-CHYMOTRYPSIN A
	Chains	:	F
	EC Number	:	3.4.21.1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 3 - GAMMA-CHYMOTRYPSIN A
	Chains	:	G
	EC Number	:	3.4.21.1
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 4 - PRO GLY ALA TYR ASP PEPTIDE
	Chains	:	B
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		1	2	3	4
Asymmetric Unit	:	B	E	F	G
Biological Unit 1 (2x)	:	B	E	F	G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 7)

No.	Name	Count	Type	Full Name
1	HEX	7	Ligand/Ion	HEXANE

Biological Unit 1 (1, 14)

No.	Name	Count	Type	Full Name
1	HEX	14	Ligand/Ion	HEXANE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE F:16 , ASN F:18 , GLY F:19 , THR F:144 , HOH F:318 , GLN G:156	BINDING SITE FOR RESIDUE HEX F 401
2	AC2	SOFTWARE	TRP F:27 , TRP F:29 , VAL F:137 , THR F:138 , THR F:139 , GLN G:157 , PRO G:198 , VAL G:200	BINDING SITE FOR RESIDUE HEX F 402
3	AC3	SOFTWARE	LEU F:97 , LEU F:143 , TYR F:146 , LYS G:175 , MET G:192 , SER G:218	BINDING SITE FOR RESIDUE HEX F 403
4	AC4	SOFTWARE	LEU E:10 , SER E:11 , ASN F:18 , HOH F:302 , GLY G:187	BINDING SITE FOR RESIDUE HEX F 404
5	AC5	SOFTWARE	PRO F:28 , GLN F:30 , VAL F:31 , SER F:32 , VAL F:67 , ALA F:68 , GLY F:69 , GLU F:70 , THR F:117 , TRP F:141 , HOH F:267	BINDING SITE FOR RESIDUE HEX F 405
6	AC6	SOFTWARE	ASP B:505 , ALA F:56 , HIS F:57 , CYS F:58 , GLY F:59 , TYR F:94 , SER F:96	BINDING SITE FOR RESIDUE HEX F 406
7	AC7	SOFTWARE	CYS E:1 , HOH E:350 , THR F:37 , HOH F:250	BINDING SITE FOR RESIDUE HEX E 407

Asymmetric Unit

No.	Residues
1	E:1	-	F:122
2	F:42	-	F:58
3	F:136	-	G:201
4	G:168	-	G:182
5	G:191	-	G:220

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

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

Asymmetric Unit (3, 3)

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

Biological Unit 1 (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	F:16-146
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CTRA_BOVIN	53-58	2	F:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CTRA_BOVIN	189-200	2	G:189-200

(no "Exon" information available for 1GMD)

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 B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1gmd B 501 PGAYD 505

Chain E from PDB  Type:PROTEIN  Length:11
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:11
                                    10 
           CTRA_BOVIN     1 CGVPAIQPVLS  11
               SCOP domains d1gmd.1     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
                 1gmd E   1 CGVPAIQPVLS  11
                                    10

Chain F 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 d1gmd.1 E:,F:,G: (alpha,gamma)-chymotrypsin(ogen)                                                                                   SCOP domains
               CATH domains 1gmdF00 F:16-146 Trypsin-like serine proteases                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeee......eeeeeeeeeeeeeee......eeeeeee...........eeeeeeeeeeee........eeeeeeeeee......................eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: F:16-146 UniProt: 16-243                                                                                          PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gmd F  16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRY 146
                                    25        35        45        55        65        75        85        95       105       115       125       135       145

Chain G from PDB  Type:PROTEIN  Length:95
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:95
                                   160       170       180       190       200       210       220       230       240     
           CTRA_BOVIN   151 TPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
               SCOP domains d1gmd.1 E:,F:,G: (alpha,gamma)-chymotrypsin(ogen)                                               SCOP domains
               CATH domains 1gmdG00 G:151-245 Trypsin-like serine proteases                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee................eeeeeeee......eeeeeeeee..........eeeeeee....eeeeeee.hhhhhhhhhhhhhhh 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
                 1gmd G 151 TPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
                                   160       170       180       190       200       210       220       230       240

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: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: (alpha,gamma)-chymotrypsin(ogen) (60)

Cow (Bos taurus) [TaxId: 9913] (58)

d1gmd.1

E:,F:,G:

Asymmetric 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	1gmdG00	G:151-245
1b	1gmdF00	F:16-146

(no "Pfam Domain" information available for 1GMD)

Asymmetric Unit(hide GO term definitions)

Chain E,F,G (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.

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Description

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Ligands, Modified Residues, Ions (1, 7)

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SS Bonds (5, 5)

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