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(-) Description

Title :  RAT ANIONIC N143H, E151H TRYPSIN COMPLEXED TO A86H ECOTIN; NICKEL-BOUND
 
Authors :  L. S. Brinen, R. J. Fletterick
Date :  07 Feb 96  (Deposition) - 11 Jul 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Serine Protease, Inhibitor, Complex, Metal Binding Sites, Protein Engineering, Protease-Substrate Interactions, Metalloproteins, Complex (Serine Protease-Inhibitor) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. S. Brinen, W. S. Willett, C. S. Craik, R. J. Fletterick
X-Ray Structures Of A Designed Binding Site In Trypsin Show Metal-Dependent Geometry.
Biochemistry V. 35 5999 1996
PubMed-ID: 8634241  |  Reference-DOI: 10.1021/BI9530200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ECOTIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneECOTIN
    Expression System PlasmidPTACTAC
    Expression System Taxid562
    GeneRAT ANIONIC TRYPSIN
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymTRYPSIN INHIBITOR
 
Molecule 2 - ANIONIC TRYPSIN
    ChainsB
    EC Number3.4.21.4
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System GeneRAT ANIONIC TRYPSIN
    Expression System PlasmidPST
    Expression System Taxid4932
    GeneRAT ANIONIC TRYPSIN
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:70 , ASN B:72 , VAL B:75 , GLU B:77 , ACT B:247BINDING SITE FOR RESIDUE CA B 246
2AC2SOFTWAREGLU B:70 , ASN B:72 , VAL B:75 , LEU B:76 , GLU B:77 , ASN B:79 , CA B:246BINDING SITE FOR RESIDUE ACT B 247
3AC3SOFTWAREHIS A:86 , HIS B:143 , HIS B:151 , HOH B:253BINDING SITE FOR RESIDUE NI B 248
4NI1UNKNOWNHIS A:86 , HIS B:143 , HIS B:151 , HOH B:253NICKEL BINDING SITE.

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:50 -A:87
2B:22 -B:157
3B:42 -B:58
4B:128 -B:232
5B:136 -B:201
6B:168 -B:182
7B:191 -B:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SLW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRY2_RAT24-244  1B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRY2_RAT59-64  1B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRY2_RAT194-205  1B:189-200
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRY2_RAT24-244  2B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRY2_RAT59-64  2B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRY2_RAT194-205  2B:189-200

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000188521ENSRNOE00000331572chr4:69088288-6908832740TRY2_RAT1-14140--
1.2bENSRNOT000000188522bENSRNOE00000277233chr4:69090744-69090903160TRY2_RAT14-67541B:16-61 (gaps)46
1.3ENSRNOT000000188523ENSRNOE00000105498chr4:69092114-69092367254TRY2_RAT67-152861B:61-145 (gaps)85
1.4ENSRNOT000000188524ENSRNOE00000338303chr4:69092772-69092908137TRY2_RAT152-197461B:150-19245
1.5ENSRNOT000000188525ENSRNOE00000134316chr4:69093163-69093367205TRY2_RAT198-246491B:193-245 (gaps)54

(-) Sequences/Alignments

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 A from PDB  Type:PROTEIN  Length:130
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:132
                                    40        50        60        70        80        90       100       110       120       130       140       150       160  
          ECOT_ECOLI     31 APYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMACPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  162
               SCOP domains d1slwa_ A: Ecotin, trypsin inhibitor                                                                                                 SCOP domains
               CATH domains 1slwA00 A:11-142  [code=2.60.40.550, no name defined]                                                                                CATH domains
               Pfam domains Ecotin-1slwA01 A:11-133                                                                                                    --------- Pfam domains
         Sec.struct. author .........eeeeee.......hhheeeeeeeeeeeee.........eeeeeee....eeeeeee..............--.eeeeee...hhhheee......eeeeee...eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1slw A   11 APYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMHCPD--KEKKFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  142
                                    20        30        40        50        60        70        80        |- |     100       110       120       130       140  
                                                                                                         89 92                                                  

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with TRY2_RAT | P00763 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:223
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            TRY2_RAT     24 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  246
               SCOP domains d1slwb_ B: Trypsin(ogen)                                                                                                                                                                                                        SCOP domains
               CATH domains 1slwB01     1slwB02 B:28-120,B:233-243 Trypsin-like serine proteases                                  1slwB01 B:16-27,B:121-2    32 Trypsin-like serine proteases                                                 1slwB02    -- CATH domains
               Pfam domains Trypsin-1slwB01 B:16-238                                                                                                                                                                                                ------- Pfam domains
         Sec.struct. author ..............eeeee...eeeeeeeee..eeee.hhh.....eee..............eeeeeeeee.............eeeee.....----...............eeeeee.....----......eeeeee...hhhhhhh........eeee................eeee..eeeeeeee..........eeeeehhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 24-244                                                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b  PDB: B:16-61 (gaps) [INCOMPLETE] ------------------------------------------------------------------------------------Exon 1.4  PDB: B:150-192 UniProt: 152-197     Exon 1.5  PDB: B:193-245 (gaps) UniProt: 198-246  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: B:61-145 (gaps) UniProt: 67-152 [INCOMPLETE]                           ---------------------------------------------------------------------------------------------- Transcript 1 (2)
                1slw B   16 IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVK----VATIALPSSCAPAGTQCLISGWGHTL----NHPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN  245
                                    25        37        47        57        68        78        88        98       108    |  118      |129||     140    |  150       160       170       180    | 188A       198     ||212    || 222       232       242   
                                             34|                           66|                                          113  118    125|  ||          145  150                               184A 188A             204|     217|  |                        
                                              37                            68                                                       127  ||                                                                        209      219  |                        
                                                                                                                                        130|                                                                                   221A                        
                                                                                                                                         132                                                                                                               

   Legend:   → Mismatch (orange background)
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    → 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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (20, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (ECOT_ECOLI | P23827)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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: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: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:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain B   (TRY2_RAT | P00763)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    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.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ECOT_ECOLI | P238271azz 1ecy 1ecz 1ezs 1ezu 1fi8 1id5 1ifg 1n8o 1p0s 1slu 1slv 1slx 1xx9 1xxd 1xxf 4iw4 4niy
        TRY2_RAT | P007631amh 1anb 1anc 1and 1ane 1bra 1brb 1brc 1co7 1dpo 1ezs 1ezu 1f5r 1f7z 1fy8 1j14 1j15 1j16 1j17 1k9o 1ql9 1slu 1slv 1slx 1trm 1ykt 1ylc 1yld 2trm 3fp6 3fp7 3fp8 3tgi 3tgj 3tgk

(-) Related Entries Specified in the PDB File

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