2A31 - JenaLib

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Title :   TRYPSIN IN COMPLEX WITH BORATE

Authors :   T. R. Transue, S. A. Gabel, R. E. London

Date :   23 Jun 05 (Deposition) - 04 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

Chains :   Asym./Biol. Unit : A

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

Reference :   T. R. Transue, S. A. Gabel, R. E. London
Nmr And Crystallographic Characterization Of Adventitious Borate Binding By Trypsin.
Bioconjug. Chem. V. 17 300 2006
PubMed-ID: 16536459 | Reference-DOI: 10.1021/BC0502210
(for further references see the PDB file header)

Molecule 1 - TRYPSIN
	Chains	:	A
	EC Number	:	3.4.21.4
	Organ	:	PANCREAS
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 9)

No.	Name	Count	Type	Full Name
1	BO4	2	Ligand/Ion	BORATE ION
2	CA	1	Ligand/Ion	CALCIUM ION
3	MG	3	Ligand/Ion	MAGNESIUM ION
4	NA	1	Ligand/Ion	SODIUM ION
5	PG3	1	Ligand/Ion	GUANIDINE-3-PROPANOL
6	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:975 , HOH A:1215	BINDING SITE FOR RESIDUE CA A 502
2	AC2	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:975 , HOH A:1215	BINDING SITE FOR RESIDUE MG A 503
3	AC3	SOFTWARE	HOH A:1115 , HOH A:1158 , HOH A:1159 , HOH A:1160 , HOH A:1161 , HOH A:1162	BINDING SITE FOR RESIDUE MG A 504
4	AC4	SOFTWARE	HOH A:1138 , HOH A:1165 , HOH A:1167 , HOH A:1168 , HOH A:1169 , HOH A:1170 , HOH A:1233	BINDING SITE FOR RESIDUE MG A 505
5	AC5	SOFTWARE	GLY A:78 , GLU A:80 , HOH A:944 , HOH A:1014 , HOH A:1151 , HOH A:1152	BINDING SITE FOR RESIDUE NA A 506
6	AC6	SOFTWARE	ARG A:66 , HOH A:1009 , HOH A:1086 , HOH A:1179 , HOH A:1183	BINDING SITE FOR RESIDUE SO4 A 511
7	AC7	SOFTWARE	SER A:164 , SER A:167 , HOH A:1092 , HOH A:1234	BINDING SITE FOR RESIDUE BO4 A 901
8	AC8	SOFTWARE	HIS A:57 , SER A:127 , ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , SER A:195 , VAL A:213 , SER A:214 , TRP A:215 , GLY A:216 , GLY A:219 , GLY A:226 , HOH A:940 , HOH A:983 , HOH A:1067 , HOH A:1214	BINDING SITE FOR RESIDUE PG3 A 501
9	AC9	SOFTWARE	SER A:37 , LYS A:60 , SER A:61 , ARG A:62 , SER A:164 , ASP A:165 , SER A:166 , HOH A:1011 , HOH A:1230 , HOH A:1235	BINDING SITE FOR RESIDUE BO4 A 512

Asymmetric/Biological Unit

No.	Residues
1	A:22	-	A:157
2	A:42	-	A:58
3	A:128	-	A:232
4	A:136	-	A:201
5	A:168	-	A:182
6	A:191	-	A:220

(no "Cis Peptide Bond" information available for 2A31)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRYP_PIG_001 *	I	20	V	TRYP_PIG	---	---	A	I	27	V
	* ID not provided by source

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	TRYP_PIG	9-229	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	TRYP_PIG	44-49	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	TRYP_PIG	179-190	1	A:189-200

(no "Exon" information available for 2A31)

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:223
 aligned with TRYP_PIG | P00761 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:223
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   
            TRYP_PIG      9 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  231
               SCOP domains d2a31a_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 2a31A01     2a31A02 A:28-120,A:233-245 Trypsin-like serine proteases                                  2a31A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     2a31A02       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eee.................eeee..eeeeeeee...........eeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 9-229                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2a31 A   16 IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN  245
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180   |   188       198     ||212    || 222       232       242   
                                             34|                            67|                                                     125|  ||                                                184A 188A              204|     217| |                         
                                              37                             69                                                      127  ||                                                                        209      219 |                         
                                                                                                                                        130|                                                                                  221A                         
                                                                                                                                         132

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: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Trypsin(ogen) (500)

Pig (Sus scrofa) [TaxId: 9823] (33)

d2a31a_

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)

Pig (Sus scrofa) (115)

1a	2a31A01	A:16-27,A:121-232
1b	2a31A02	A:28-120,A:233-245

(no "Pfam Domain" information available for 2A31)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRYP_PIG | P00761)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.

Asymmetric/Biological Unit
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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 9)

Sites (9, 9)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (1, 1)

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