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(-) Description

Title :  STRUCTURE OF A BPTI-[5,55] VARIANT CONTAINING GLY/VAL AT THE 14/38TH POSITIONS
 
Authors :  M. M. Islam, S. Sohya, K. Noguchi, M. Yohda, Y. Kuroda
Date :  24 Nov 08  (Deposition) - 13 Oct 09  (Release) - 27 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Folding, Protein Stabilization, Protein Design, Pharmaceutical, Protease Inhibitor, Secreted, Serine Protease Inhibitor, Hydrolase Inhibitor, Disulfide Bond (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Islam, S. Sohya, K. Noguchi, S. Kidokoro, M. Yohda, Y. Kuroda
Thermodynamic And Structural Analysis Of Highly Stabilized Bptis By Single And Double Mutations
Proteins V. 77 962 2009
PubMed-ID: 19830687  |  Reference-DOI: 10.1002/PROT.22522
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PANCREATIC TRYPSIN INHIBITOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: BASIC PROTEASE INHIBITOR, BPTI, BPI, APROTININ

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:4 , LYS A:41 , ARG A:42 , ARG A:53 , HOH A:66 , HOH A:76 , HOH A:98 , HOH A:101 , ARG B:39BINDING SITE FOR RESIDUE SO4 A 4001
2AC2SOFTWAREARG A:20 , TYR A:35 , GLY A:37 , ALA A:40 , HOH A:130 , HOH A:137 , ARG B:42BINDING SITE FOR RESIDUE SO4 A 4002
3AC3SOFTWAREARG A:42 , HOH A:133 , ARG B:20 , TYR B:35 , ALA B:40 , HOH B:89 , HOH B:97 , HOH B:113BINDING SITE FOR RESIDUE SO4 B 4003

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:55
2B:5 -B:55

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZVX)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.BPT1_BOVIN40-90
 		  2A:5-55
B:5-55
2BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.BPT1_BOVIN68-86
 		  2A:33-50
B:33-50

(-) Exons   (0, 0)

(no "Exon" information available for 2ZVX)

(-) 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:58
 aligned with BPT1_BOVIN | P00974 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:58
                                    45        55        65        75        85        
            BPT1_BOVIN   36 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA 93
               SCOP domains d2zvxa_ A: automated matches                               SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee....eeeeeee...........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----BPTI_KUNITZ_2  PDB: A:5-55 UniProt: 40-90          --- PROSITE (1)
                PROSITE (2) --------------------------------BPTI_KUNITZ_1      ------- PROSITE (2)
                 Transcript ---------------------------------------------------------- Transcript
                  2zvx A  1 RPDFCLEPPYTGPGKARIIRYFYNAKAGLAQTFVYGGVRAKRNNFKSAEDALRTCGGA 58
                                    10        20        30        40        50        


Chain B from PDB  Type:PROTEIN  Length:57
 aligned with BPT1_BOVIN | P00974 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:57
                                    45        55        65        75        85       
            BPT1_BOVIN   36 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGG 92
               SCOP domains d2zvxb_ B: automated matches                              SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
           Pfam domains (1) ---Kunitz_BPTI-2zvxB01 B:4-56                           - Pfam domains (1)
           Pfam domains (2) ---Kunitz_BPTI-2zvxB02 B:4-56                           - Pfam domains (2)
         Sec.struct. author .hhhhhh..........eeeeeee....eeeeeee...........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----BPTI_KUNITZ_2  PDB: B:5-55 UniProt: 40-90          -- PROSITE (1)
                PROSITE (2) --------------------------------BPTI_KUNITZ_1      ------ PROSITE (2)
                 Transcript --------------------------------------------------------- Transcript
                  2zvx B  1 RPDFCLEPPYTGPGKARIIRYFYNAKAGLAQTFVYGGVRAKRNNFKSAEDALRTCGG 57
                                    10        20        30        40        50
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZVX)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Protease_inhib (47)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BPT1_BOVIN | P00974)
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:0019870    potassium channel inhibitor activity    Stops, prevents, or reduces the activity of a potassium channel.
    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.
    GO:0090331    negative regulation of platelet aggregation    Any process that decreases the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0070495    negative regulation of thrombin-activated receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of thrombin-activated receptor protein signaling pathway activity. A thrombin receptor signaling pathway is the series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
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.

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  2zvx
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 Related Entries

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

UniProtKB/Swiss-Prot
        BPT1_BOVIN | P00974: 1aal 1b0c 1bhc 1bpi 1bpt 1brb 1bth 1bti 1bz5 1bzx 1cbw 1co7 1d0d 1eaw 1ejm 1f5r 1f7z 1fak 1fan 1fy8 1g6x 1jv8 1jv9 1k09 1k6u 1ld5 1ld6 1mtn 1nag 1oa5 1oa6 1p2i 1p2j 1p2k 1p2m 1p2n 1p2o 1p2q 1pit 1qlq 1t7c 1t8l 1t8m 1t8n 1t8o 1tpa 1uua 1uub 1ykt 1ylc 1yld 2fi3 2fi4 2fi5 2ftl 2ftm 2hex 2ijo 2kai 2ptc 2r9p 2ra3 2tgp 2tpi 2zjx 3btd 3bte 3btf 3btg 3bth 3btk 3btm 3btq 3btt 3btw 3fp6 3fp7 3fp8 3gym 3ldi 3ldj 3ldm 3otj 3p92 3p95 3tgi 3tgj 3tgk 3tpi 3u1j 3wny 4bnr 4dg4 4pti 4tpi 4wwy 4wxv 4y0y 4y0z 4y10 4y11 5jb4 5jb5 5jb6 5jb7 5pti 6pti 7pti 8pti 9pti

(-) Related Entries Specified in the PDB File

2zjx BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) CONTAINING ONLY THE [5,55] DISULFIDE BONDD
3ci7 CRYSTAL STRUCTURE OF A SIMPLIFIED BPTI CONTAINING 20 ALANINES