3LDM - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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) - 23 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E  (2x)

Keywords :   Aprotinin, Sucrose Octasulfate, 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 Sucrose Octasulfate Reveal Multiple Modes Of Interactions With Implications For Heparin Binding.
Biochem. Biophys. Res. Commun. 2010
PubMed-ID: 20529698 | Reference-DOI: 10.1016/J.BBRC.2010.05.113

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

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3LDM)

(no "Site" information available for 3LDM)

Asymmetric Unit

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

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

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

Asymmetric Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BPTI_KUNITZ_2	PS50279	Pancreatic trypsin inhibitor (Kunitz) family profile.	BPT1_BOVIN	40-90	5	A:5-55 B:5-55 C:5-55 D:5-55 E:5-55
2	BPTI_KUNITZ_1	PS00280	Pancreatic trypsin inhibitor (Kunitz) family signature.	BPT1_BOVIN	68-86	5	A:33-51 B:33-51 C:33-51 D:33-51 E:33-51

Biological Unit 1 (2, 20)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BPTI_KUNITZ_2	PS50279	Pancreatic trypsin inhibitor (Kunitz) family profile.	BPT1_BOVIN	40-90	10	A:5-55 B:5-55 C:5-55 D:5-55 E:5-55
2	BPTI_KUNITZ_1	PS00280	Pancreatic trypsin inhibitor (Kunitz) family signature.	BPT1_BOVIN	68-86	10	A:33-51 B:33-51 C:33-51 D:33-51 E:33-51

(no "Exon" information available for 3LDM)

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: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 d3ldma_ 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
                  3ldm A  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG 56
                                    10        20        30        40        50

Chain B 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 d3ldmb_ B: Pancreatic trypsin inhibitor, BPTI            SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..........eeeeeee....eeeeeee...........hhhhhhhhh. 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
                  3ldm B  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG 56
                                    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 d3ldmc_ 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
                  3ldm C  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG 56
                                    10        20        30        40        50

Chain D 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 d3ldmd_ D: Pancreatic trypsin inhibitor, BPTI            SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..........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
                  3ldm D  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG 56
                                    10        20        30        40        50

Chain E 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 d3ldme_ E: Pancreatic trypsin inhibitor, BPTI            SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...........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
                  3ldm E  1 RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG 56
                                    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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: BPTI-like (161)

Superfamily: BPTI-like (161)

Family: Small Kunitz-type inhibitors & BPTI-like toxins (128)

Protein domain: Pancreatic trypsin inhibitor, BPTI (85)

Cow (Bos taurus) [TaxId: 9913] (85)

1a	d3ldma_	A:
1b	d3ldmb_	B:
1c	d3ldmc_	C:
1d	d3ldmd_	D:
1e	d3ldme_	E:

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

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

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 3ldm)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ldm)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (15, 15)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 10)

Exons (0, 0)

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SCOP Domains (1, 5)

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Gene Ontology (9, 9)

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