3BG4 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF GUAMERIN IN COMPLEX WITH CHYMOTRYPSIN AND THE DEVELOPMENT OF AN ELASTASE-SPECIFIC INHIBITOR

Authors :   H. Kim, T. T. T. Chu, D. Y. Kim, D. R. Kim, C. M. T. Nguyen, J. Choi, J. R. Lee, M. J. Hahn, K. K. Kim

Date :   26 Nov 07 (Deposition) - 29 Jul 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Guamerin, Chymotrypsin, Elastase, Inhibitor, Digestion, Hydrolase, Protease, Secreted, Serine Protease, Zymogen, Protease Inhibitor, Serine Protease Inhibitor, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Kim, T. T. T. Chu, D. Y. Kim, D. R. Kim, C. M. T. Nguyen, J. Choi, J. R. Lee, M. J. Hahn, K. K. Kim
The Crystal Structure Of Guamerin In Complex With Chymotrypsin And The Development Of An Elastase-Specific Inhibitor.
J. Mol. Biol. V. 376 184 2008
PubMed-ID: 18155725 | Reference-DOI: 10.1016/J.JMB.2007.11.089
(for further references see the PDB file header)

Molecule 1 - CHYMOTRYPSIN A CHAIN A
	Chains	:	A
	EC Number	:	3.4.21.1
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 2 - CHYMOTRYPSIN A CHAIN B
	Chains	:	B
	EC Number	:	3.4.21.1
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 3 - CHYMOTRYPSIN A CHAIN C
	Chains	:	C
	EC Number	:	3.4.21.1
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 4 - GUAMERIN
	Chains	:	D
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Organism Common	:	LEECH
	Organism Scientific	:	HIRUDO NIPPONIA
	Organism Taxid	:	42736

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3BG4)

(no "Site" information available for 3BG4)

Asymmetric/Biological Unit

No.	Residues
1	A:1	-	B:122
2	B:42	-	B:58
3	B:136	-	C:201
4	C:168	-	C:182
5	C:191	-	C:220
6	D:12	-	D:23
7	D:17	-	D:28
8	D:30	-	D:50
9	D:35	-	D:54
10	D:39	-	D:56

(no "Cis Peptide Bond" information available for 3BG4)

(no "SAP(SNP)/Variant" information available for 3BG4)

Asymmetric/Biological Unit (4, 4)

	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	B:16-146
2	ANTISTASIN	PS51252	Antistasin-like domain profile.	GUAM_HIRNI	30-56	1	D:30-56
3	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CTRA_BOVIN	53-58	1	B:53-58
4	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CTRA_BOVIN	189-200	1	C:189-200

(no "Exon" information available for 3BG4)

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:11
 aligned with CTRB_BOVIN | P00767 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:11
                                    10 
           CTRB_BOVIN     1 CGVPAIQPVLS  11
               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
                 3bg4 A   1 CGVPAIQPVLS  11
                                    10

Chain B 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 3bg4B00 B:16-146 Trypsin-like serine proteases                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeee....eeeehhhhh.....eeee............eeeeeeeeee.............eeeee..........................eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-146 UniProt: 16-243                                                                                          PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------TRYPSI---------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bg4 B  16 IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRY 146
                                    25        35        45        55        65        75        85        95       105       115       125       135       145

Chain C 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 3bg4C00 C:149-245 Trypsin-like serine proteases                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeehhhhhhhhhhhhh...eeeee.............eeeeee..eeeeeeeeeeee.......eeeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: - UniProt: 16-243                                                            -- PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3bg4 C 149 ANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN 245
                                   158       168       178       188       198       208       218       228       238

Chain D from PDB  Type:PROTEIN  Length:46
 aligned with GUAM_HIRNI | P46443 from UniProtKB/Swiss-Prot  Length:57

    Alignment length:46
                                    21        31        41        51      
           GUAM_HIRNI    12 CGEKTCSPAQVCLNNECACTAIRCMIFCPNGFKVDENGCEYPCTCA  57
               SCOP domains d3bg4d_ D: automated matches                   SCOP domains
               CATH domains 3bg4D00 D:12-57 Antistasin; domain 1           CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .........eee....eee..eee.......eee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------ANTISTASIN  PDB: D:30-56   - PROSITE (2)
                 Transcript ---------------------------------------------- Transcript
                 3bg4 D  12 CGEKTCSPAQVCLNNECACTAIRCMIFCPNGFKVDENGCEYPCTCA  57
                                    21        31        41        51

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: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: Leech antihemostatic proteins (21)

Family: automated matches (1)

Protein domain: automated matches (1)

Hirudo nipponia [TaxId: 42736] (1)

d3bg4d_

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)

Bovine (Bos taurus) (36)

1a	3bg4C00	C:149-245
1b	3bg4B00	B:16-146

Architecture: Ribbon (789)

Topology: Antistasin; domain 1 (8)

Homologous Superfamily: Antistasin; domain 1 (8)

Bovine (Bos taurus) (1)

3bg4D00

D:12-57

(no "Pfam Domain" information available for 3BG4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CTRB_BOVIN | P00767)

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: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.

Chain B,C (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.

Chain D (GUAM_HIRNI | P46443)

molecular function
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0050819	negative regulation of coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bg4)

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(no "Related Entries Specified in the PDB File" available for 3BG4)

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (10, 10)

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