5PTP - JenaLib

Title :   STRUCTURE OF HYDROLASE (SERINE PROTEINASE)

Authors :   R. M. Stroud, J. Finer-Moore

Date :   31 Mar 97 (Deposition) - 07 Jul 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.34

Chains :   Asym./Biol. Unit : A

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

Reference :   J. S. Finer-Moore, A. A. Kossiakoff, J. H. Hurley, T. Earnest, R. M. Stroud
Solvent Structure In Crystals Of Trypsin Determined By X-Ray And Neutron Diffraction.
Proteins V. 12 203 1992
PubMed-ID: 1557349 | Reference-DOI: 10.1002/PROT.340120302
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:70 , ASN A:72 , VAL A:75 , GLU A:80 , HOH A:290 , HOH A:291	BINDING SITE FOR RESIDUE CA A 247
2	BIN	UNKNOWN	ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , SER A:214 , TRP A:215 , GLY A:216 , SER A:217 , GLY A:219 , CYS A:220	IS THE SPECIFIC BINDING POCKET. ASP 189 AT THE BOTTOM OF THIS POCKET FORMS AN H-BOND TO THE POSITIVELY CHARGED SIDE CHAIN OF A SPECIFIC SUBSTRATE, GIVING TRYPSIN ITS SPECIFICITY FOR THIS TYPE OF SIDE CHAIN. THE BACKBONE IN THE REGION FROM SER 214 TO CYS 220 IS INVOLVED IN HYDROGEN BONDING TO A PEPTIDE SUBSTRATE.
3	CAT	UNKNOWN	HIS A:57 , ASP A:102 , GLY A:193 , MIS A:195	THE CATALYTIC SITE. IT IS COMPOSED OF RESIDUES ASP 102, HIS 57 AND MIS 195. THE OG ATOM OF MIS 195 NUCLEOPHILICALLY ATTACKS THE SUBSTRATE CARBONYL CARBON ATOM. ASP 102 AND HIS 57 TOGETHER PROVIDE GENERAL BASE CATALYSIS. THE N-H GROUPS OF GLY 193 AND MIS 195 STABILIZE REACTION INTERMEDIATES THROUGH H-BONDS TO THE SUBSTRATE CARBONYL OXYGEN ATOM.
4	ION	UNKNOWN	GLU A:70 , ASP A:71 , ASN A:72 , ILE A:73 , ASN A:74 , VAL A:75 , VAL A:76 , GLU A:77 , GLY A:78 , ASN A:79 , GLU A:80	CONTAINS A TIGHTLY BOUND POSITIVE ION WHICH IS PROBABLY A CA2+ IN THIS STRUCTURE. THE ION IS GIVEN SEQUENCE IDENTIFIER CA 247 AND OCCURS AMONG THE WATER MOLECULES AT THE END OF THIS ENTRY. THE ION IS COORDINATED IN A ROUGHLY OCTAHEDRAL FASHION BY GLU 70, ASN 72, VAL 75, GLU 80, HOH 341 AND HOH 342 AS SPECIFIED IN THE LINK RECORDS. THIS REGION WAS FIRST IDENTIFIED AS THE PRIMARY CA2+ BINDING SITE OF TRYPSIN BY BODE AND SCHWAGER, F.E.B.S. LETT., VOL. 56, P139 (1975).

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains d5ptpa_ A: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 5ptpA01     5ptpA02 A:28-120,A:233-244 Trypsin-like serine proteases                                  5ptpA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     5ptpA02     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee...eeeeeeeee..eeee.hhh.....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee...hhhhhhh........eeee................eeee..eeeeeeee..........eeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ptp A   16 IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDsGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN  245
                                    25        37        47        57        66|       78        88        98       108       118      |129||     140       150       160       170       180    | 188A      |198     ||212    || 222       232       242   
                                             34|                          65A||                                                     125|  ||                                                 184A 188A      |      204|     217|  |                        
                                              37                            66|                                                      127  ||                                                              195-MIS   209      219  |                        
                                                                             69                                                         130|                                                                                   221A                        
                                                                                                                                         132

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	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 (0, 0)

Gene Ontology (10, 10)

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