1S84 - JenaLib

Title :   PORCINE TRYPSIN COVALENT COMPLEX WITH 4-AMINO BUTANOL, BORATE AND ETHYLENE GLYCOL

Authors :   T. R. Transue, J. M. Krahn, S. A. Gabel, E. F. Derose, R. E. London

Date :   30 Jan 04 (Deposition) - 16 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

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

Reference :   T. R. Transue, J. M. Krahn, S. A. Gabel, E. F. Derose, R. E. London
X-Ray And Nmr Characterization Of Covalent Complexes Of Trypsin, Borate, And Alcohols.
Biochemistry V. 43 2829 2004
PubMed-ID: 15005618 | Reference-DOI: 10.1021/BI035782Y
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:80 , HOH A:295 , HOH A:327	BINDING SITE FOR RESIDUE CA A 1
02	AC2	SOFTWARE	ASN A:48 , ARG A:66 , HOH A:433 , HOH A:490 , HOH A:519	BINDING SITE FOR RESIDUE SO4 A 2
03	AC3	SOFTWARE	ASN A:95 , ASN A:97 , THR A:98	BINDING SITE FOR RESIDUE SO4 A 3
04	AC4	SOFTWARE	SER A:37 , LYS A:60 , ASP A:165 , SER A:166 , HOH A:480 , HOH A:515	BINDING SITE FOR RESIDUE SO4 A 4
05	AC5	SOFTWARE	ARG A:125 , TYR A:217 , HOH A:400 , HOH A:415 , HOH A:416 , HOH A:443	BINDING SITE FOR RESIDUE EDO A 5
06	AC6	SOFTWARE	ASN A:97 , ARG A:125 , GLN A:204 , HOH A:380 , HOH A:400 , HOH A:403	BINDING SITE FOR RESIDUE EDO A 6
07	AC7	SOFTWARE	GLY A:96 , ASN A:97 , ARG A:125 , SER A:127 , GLN A:204 , GLN A:210 , HOH A:385	BINDING SITE FOR RESIDUE EDO A 7
08	AC8	SOFTWARE	ASN A:34 , GLY A:38 , SER A:39 , HIS A:40 , ILE A:73 , ASP A:74 , HOH A:516 , HOH A:519 , HOH A:520 , HOH A:521	BINDING SITE FOR RESIDUE EDO A 8
09	AC9	SOFTWARE	ILE A:47 , ASN A:48 , LEU A:123 , TYR A:217 , HOH A:431	BINDING SITE FOR RESIDUE EDO A 9
10	BC1	SOFTWARE	HIS A:91 , ASN A:101 , SER A:149 , ASN A:179 , ASN A:233 , HOH A:309 , HOH A:344 , HOH A:438	BINDING SITE FOR RESIDUE EDO A 10
11	BC2	SOFTWARE	HIS A:57 , ASP A:189 , SER A:190 , CYS A:191 , GLY A:193 , SER A:195 , HOH A:283 , HOH A:303 , HOH A:381 , HOH A:383	BINDING SITE FOR RESIDUE DYB A 11

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

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 d1s84a_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1s84A01     1s84A02 A:28-120,A:233-245 Trypsin-like serine proteases                                  1s84A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1s84A02       CATH domains
               Pfam domains Trypsin-1s84A01 A:16-238                                                                                                                                                                                                ------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...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
                1s84 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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DYB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s84)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1s84
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TRYP_PIG \| P00761
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.21.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description