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(-) Description

Title :  CRYSTAL STRUCTURE OF APROTININ IN COMPLEX WITH SUCROSE OCTASULFATE: UNUSUAL INTERACTIONS AND IMPLICATION FOR HEPARIN BINDING
 
Authors :  I. S. Yang, T. G. Kim, B. S. Park, K. H. Kim
Date :  13 Jan 10  (Deposition) - 23 Jun 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  Aprotinin, Sucrose Octasulfate, Disulfide Bond, Protease Inhibitor, Secreted, Serine Protease Inhibitor, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. S. Yang, T. G. Kim, B. S. Park, K. J. Cho, J. -H. Lee, Y. Park, K. H. Kim
Crystal Structures Of Aprotinin And Its Complex With Sucros Octasulfate Reveal Multiple Modes Of Interactions With Implications For Heparin Binding
Biochem. Biophys. Res. Commun. V. 397 429 2010
PubMed-ID: 20529698  |  Reference-DOI: 10.1016/J.BBRC.2010.05.113

(-) Compounds

Molecule 1 - PANCREATIC TRYPSIN INHIBITOR
    Chains: A, B, C, D, E
    Fragment: UNP RESIDUES 36-93
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: BASIC PROTEASE INHIBITOR, BPTI, BPI, APROTININ

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric Unit (3, 25)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HG5Ligand/IonMERCURY (II) ION
3SO418Ligand/IonSULFATE ION
Biological Unit 1 (2, 40)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2HG-1Ligand/IonMERCURY (II) ION
3SO436Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:7 , ARG A:42 , HOH A:89 , HOH A:144BINDING SITE FOR RESIDUE SO4 A 59
02AC2SOFTWAREILE A:18 , ARG A:20 , LYS A:46 , HOH A:106BINDING SITE FOR RESIDUE SO4 A 60
03AC3SOFTWAREPRO A:2 , HOH A:75 , PRO E:2 , ASP E:3 , HOH E:69BINDING SITE FOR RESIDUE SO4 A 61
04AC4SOFTWAREARG A:42 , HOH A:85 , ARG E:1BINDING SITE FOR RESIDUE SO4 A 62
05AC5SOFTWARECYS A:30BINDING SITE FOR RESIDUE HG A 63
06AC6SOFTWAREGLU B:7 , LYS B:41 , ARG B:42 , HOH B:78 , HOH B:86BINDING SITE FOR RESIDUE SO4 B 59
07AC7SOFTWAREILE B:18 , ARG B:20 , HOH B:134 , HOH C:178 , HOH C:183BINDING SITE FOR RESIDUE SO4 B 60
08AC8SOFTWARELYS B:26 , ARG B:42 , HOH B:68 , HOH D:174BINDING SITE FOR RESIDUE SO4 B 61
09AC9SOFTWARECYS B:14 , CYS B:38 , GOL B:63 , PRO C:9 , PHE C:22 , PHE C:33 , HOH C:63BINDING SITE FOR RESIDUE SO4 B 62
10BC1SOFTWARESO4 B:62BINDING SITE FOR RESIDUE GOL B 63
11BC2SOFTWARECYS B:30 , ARG E:53BINDING SITE FOR RESIDUE HG B 64
12BC3SOFTWARELYS C:41 , ARG C:42 , HOH C:156BINDING SITE FOR RESIDUE SO4 C 59
13BC4SOFTWAREILE C:18 , ARG C:20 , LYS C:46BINDING SITE FOR RESIDUE SO4 C 60
14BC5SOFTWAREARG C:1 , ARG C:42 , HOH C:75BINDING SITE FOR RESIDUE GOL C 61
15BC6SOFTWAREHOH B:84 , CYS C:30BINDING SITE FOR RESIDUE HG C 62
16BC7SOFTWAREGLU D:7 , ARG D:42 , HOH D:88 , HOH D:163BINDING SITE FOR RESIDUE SO4 D 59
17BC8SOFTWAREILE D:18 , ARG D:20 , LYS D:46 , HOH D:93BINDING SITE FOR RESIDUE SO4 D 60
18BC9SOFTWARELYS C:46 , SER C:47 , ALA C:48 , GLU C:49 , HOH C:108 , TYR D:21 , SER D:47 , ALA D:48BINDING SITE FOR RESIDUE SO4 D 61
19CC1SOFTWAREARG D:42 , HOH D:65 , HOH D:77 , LYS E:26BINDING SITE FOR RESIDUE SO4 D 62
20CC2SOFTWARELEU D:29 , CYS D:30BINDING SITE FOR RESIDUE HG D 63
21CC3SOFTWAREGLU E:7 , LYS E:41 , ARG E:42 , HOH E:111BINDING SITE FOR RESIDUE SO4 E 59
22CC4SOFTWAREILE A:19 , HOH A:145 , ILE E:18 , ARG E:20 , HOH E:141BINDING SITE FOR RESIDUE SO4 E 60
23CC5SOFTWARELYS A:46 , HOH A:84 , TYR B:21 , ALA B:48 , SER E:47 , ALA E:48 , GLU E:49BINDING SITE FOR RESIDUE SO4 E 61
24CC6SOFTWARELYS D:26 , ARG E:42 , HOH E:69 , HOH E:180BINDING SITE FOR RESIDUE SO4 E 62
25CC7SOFTWARECYS E:30 , HOH E:100BINDING SITE FOR RESIDUE HG E 63

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:5 -A:55
2A:14 -A:38
3A:30 -A:51
4B:5 -B:55
5B:14 -B:38
6B:30 -B:51
7C:5 -C:55
8C:14 -C:38
9C:30 -C:51
10D:5 -D:55
11D:14 -D:38
12D:30 -D:51
13E:5 -E:55
14E:14 -E:38
15E:30 -E:51

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LDI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LDI)

(-) PROSITE Motifs  (2, 10)

Asymmetric Unit (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.BPT1_BOVIN40-90
 
 
 
 		  5A:5-55
B:5-55
C:5-55
D:5-55
E:5-55
2BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.BPT1_BOVIN68-86
 
 
 
 		  5A:33-51
B:33-51
C:33-51
D:33-51
E:33-51
Biological Unit 1 (2, 20)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.BPT1_BOVIN40-90
 
 
 
 		  10A:5-55
B:5-55
C:5-55
D:5-55
E:5-55
2BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.BPT1_BOVIN68-86
 
 
 
 		  10A:33-51
B:33-51
C:33-51
D:33-51
E:33-51

(-) Exons   (0, 0)

(no "Exon" information available for 3LDI)

(-) 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: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 d3ldia_ A: Pancreatic trypsin inhibitor, BPTI             SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..........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
                  3ldi A  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGG 57
                                    10        20        30        40        50       


Chain B 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 d3ldib_ B: Pancreatic trypsin inhibitor, BPTI              SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         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
                  3ldi B  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA 58
                                    10        20        30        40        50        


Chain C from PDB  Type:PROTEIN  Length:56
 aligned with BPT1_BOVIN | P00974 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:56
                                    45        55        65        75        85      
            BPT1_BOVIN   36 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG 91
               SCOP domains d3ldic_ C: Pancreatic trypsin inhibitor, BPTI            SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..........eeeeeee....eeeeeee...........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----BPTI_KUNITZ_2  PDB: C:5-55 UniProt: 40-90          - PROSITE (1)
                PROSITE (2) --------------------------------BPTI_KUNITZ_1      ----- PROSITE (2)
                 Transcript -------------------------------------------------------- Transcript
                  3ldi C  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG 56
                                    10        20        30        40        50      


Chain D 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 d3ldid_ D: Pancreatic trypsin inhibitor, BPTI              SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..........eeeeeee....eeeeeee...........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----BPTI_KUNITZ_2  PDB: D:5-55 UniProt: 40-90          --- PROSITE (1)
                PROSITE (2) --------------------------------BPTI_KUNITZ_1      ------- PROSITE (2)
                 Transcript ---------------------------------------------------------- Transcript
                  3ldi D  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA 58
                                    10        20        30        40        50        


Chain E 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 d3ldie_ E: Pancreatic trypsin inhibitor, BPTI             SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..........eeeeeee....eeeeeee...........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----BPTI_KUNITZ_2  PDB: E:5-55 UniProt: 40-90          -- PROSITE (1)
                PROSITE (2) --------------------------------BPTI_KUNITZ_1      ------ PROSITE (2)
                 Transcript --------------------------------------------------------- Transcript
                  3ldi E  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGG 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, 5)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LDI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LDI)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (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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 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 2zvx 3btd 3bte 3btf 3btg 3bth 3btk 3btm 3btq 3btt 3btw 3fp6 3fp7 3fp8 3gym 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

3ldj 3ldm