1GMH - JenaLib

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Title :   REFINED CRYSTAL STRUCTURE OF "AGED" AND "NON-AGED" ORGANOPHOSPHORYL CONJUGATES OF GAMMA-CHYMOTRYPSIN

Authors :   M. Harel, J. L. Sussman, I. Silman

Date :   01 Jul 94 (Deposition) - 30 Sep 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : E,F,G
Biol. Unit 1: E,F,G  (1x)
Biol. Unit 2: E,F,G  (2x)
Biol. Unit 3: E (2x),F (2x),G (2x)

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

Reference :   M. Harel, C. T. Su, F. Frolow, Y. Ashani, I. Silman, J. L. Sussman
Refined Crystal Structures Of "Aged" And "Non-Aged" Organophosphoryl Conjugates Of Gamma-Chymotrypsin.
J. Mol. Biol. V. 221 909 1991
PubMed-ID: 1942036 | Reference-DOI: 10.1016/0022-2836(91)80183-U
(for further references see the PDB file header)

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ISP	1	Ligand/Ion	PHOSPHORYLISOPROPANE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ISP	1	Ligand/Ion	PHOSPHORYLISOPROPANE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	ISP	2	Ligand/Ion	PHOSPHORYLISOPROPANE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ISP	-1	Ligand/Ion	PHOSPHORYLISOPROPANE
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP G:153 , ARG G:154	BINDING SITE FOR RESIDUE SO4 G 299
2	AC2	SOFTWARE	LYS F:36 , SER F:92 , HOH F:334 , TRP G:237	BINDING SITE FOR RESIDUE SO4 F 300
3	AC3	SOFTWARE	HIS F:57 , CYS G:191 , MET G:192 , GLY G:193 , ASP G:194 , SER G:195 , SER G:214 , TRP G:215	BINDING SITE FOR RESIDUE ISP G 290
4	CAT	AUTHOR	HIS F:57 , ASP F:102 , SER G:195	RESIDUES WHICH FORM THE CATALYTIC CENTER OF THE MOLECULE

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 1GMH)

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

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, 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 2 (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

Biological Unit 3 (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 1GMH)

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 E 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 d1gmh.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
                 1gmh E   1 CGVPAIQPVL  10
                                    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 d1gmh.1 E:,F:,G: (alpha,gamma)-chymotrypsin(ogen)                                                                                   SCOP domains
               CATH domains 1gmhF00 F: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: F:16-146 UniProt: 16-243                                                                                          PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gmh F  16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRY 146
                                    25        35        45        55        65        75        85        95       105       115       125       135       145

Chain G from PDB  Type:PROTEIN  Length:96
 aligned with CTRA_BOVIN | P00766 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:96
                                   159       169       179       189       199       209       219       229       239      
           CTRA_BOVIN   150 NTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
               SCOP domains d1gmh.1 E:,F:,G: (alpha,gamma)-chymotrypsin(ogen)                                                SCOP domains
               CATH domains 1gmhG00 G:150-245 Trypsin-like serine proteases                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee..hhhhhhhhhhhhh...eeeee.............eeeeee..eeeeeeeeee.........eeeeee...hhhhhhhhhhh. 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
                 1gmh G 150 NTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
                                   159       169       179       189       199       209       219       229       239

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(

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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)

d1gmh.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	1gmhG00	G:150-245
1b	1gmhF00	F:16-146

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

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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(no "Related Entries Specified in the PDB File" available for 1GMH)

Description

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Ligands, Modified Residues, Ions (2, 3)

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