3BPM - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FALCIPAIN-3 WITH ITS INHIBITOR, LEUPEPTIN

Authors :   I. D. Kerr, J. H. Lee, L. S. Brinen

Date :   18 Dec 07 (Deposition) - 30 Dec 08 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Falcipain, Malaria, Cysteine Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. D. Kerr, J. H. Lee, K. C. Pandey, A. Harrison, M. Sajid, P. J. Rosenthal, L. S. Brinen
Structures Of Falcipain-2 And Falcipain-3 Bound To Small Molecule Inhibitors: Implications For Substrate Specificity
J. Med. Chem. V. 52 852 2009
PubMed-ID: 19128015 | Reference-DOI: 10.1021/JM8013663

Molecule 1 - CYSTEINE PROTEASE FALCIPAIN-3
	Chains	:	A, B
	EC Number	:	3.4.22.-
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833

Molecule 2 - LEUPEPTIN
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	STREPTOMYCES ROSEUS
	Organism Taxid	:	66430
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	AR7	2	Mod. Amino Acid	AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	AR7	1	Mod. Amino Acid	AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	AR7	1	Mod. Amino Acid	AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:20 , ALA A:24 , LYS A:25 , LEU A:26 , ARG A:28	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	ALA A:24 , LYS A:25 , ARG A:150 , HOH A:419	BINDING SITE FOR RESIDUE SO4 A 302
3	AC3	SOFTWARE	ARG A:202 , ARG B:28	BINDING SITE FOR RESIDUE SO4 A 303
4	AC4	SOFTWARE	ARG A:202 , LYS B:20 , LYS B:25 , LEU B:26 , ARG B:28	BINDING SITE FOR RESIDUE SO4 B 301
5	AC5	SOFTWARE	ARG B:150	BINDING SITE FOR RESIDUE SO4 B 302
6	AC6	SOFTWARE	GLN B:45 , GLY B:49 , SER B:50 , CYS B:51 , TRP B:52 , TYR B:90 , GLY B:91 , GLY B:92 , TYR B:93 , ASN B:182 , HIS B:183	BINDING SITE FOR CHAIN C OF LEUPEPTIN
7	AC7	SOFTWARE	GLN A:45 , GLY A:49 , SER A:50 , CYS A:51 , TRP A:52 , TYR A:90 , GLY A:91 , GLY A:92 , TYR A:93 , ASP A:164 , GLU A:176 , ASN A:182 , HIS A:183 , HOH A:405 , HOH A:408 , HOH D:101 , HOH D:102 , HOH D:103	BINDING SITE FOR CHAIN D OF LEUPEPTIN

Asymmetric Unit

No.	Residues
1	A:48	-	A:89
2	A:82	-	A:123
3	A:108	-	A:128
4	A:177	-	A:238
5	B:48	-	B:89
6	B:82	-	B:123
7	B:108	-	B:128
8	B:177	-	B:238

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

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

(no "PROSITE Motif" information available for 3BPM)

(no "Exon" information available for 3BPM)

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:243
 aligned with Q9NAW4_PLAFA | Q9NAW4 from UniProtKB/TrEMBL  Length:492

    Alignment length:243
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489   
         Q9NAW4_PLAFA   250 YEANYEDVIKKYKPADAKLDRIAYDWRLHGGVTPVKDQALCGSCWAFSSVGSVESQYAIRKKALFLFSEQELVDCSVKNNGCYGGYITNAFDDMIDLGGLCSQDDYPYVSNLPETCNLKRCNERYTIKSYVSIPDDKFKEALRYLGPISISIAASDDFAFYRGGFYDGECGAAPNHAVILVGYGMKDIYNEDTGRMEKFYYYIIKNSWGSDWGEGGYINLETDENGYKKTCSIGTEAYVPLLE 492
               SCOP domains d3bpma_ A: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 3bpmA00 A:8-250 Cysteine proteinases                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh..........ee.hhh.............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhh..ee...............hhhhh..ee...eeee....hhhhhhhhh..eeeee..hhhhhhh..............eeeeeeeeeeeeee......eeeeeeeeee...........eeeeee......hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bpm A   8 YEANYEDVIKKYKPADAKLDRIAYDWRLHGGVTPVKDQALCGSCWAFSSVGSVESQYAIRKKALFLFSEQELVDCSVKNNGCYGGYITNAFDDMIDLGGLCSQDDYPYVSNLPETCNLKRCNERYTIKSYVSIPDDKFKEALRYLGPISISIAASDDFAFYRGGFYDGECGAAPNHAVILVGYGMKDIYNEDTGRMEKFYYYIIKNSWGSDWGEGGYINLETDENGYKKTCSIGTEAYVPLLE 250
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain A from PDB  Type:PROTEIN  Length:243
 aligned with Q9NBA7_PLAFA | Q9NBA7 from UniProtKB/TrEMBL  Length:488

    Alignment length:243
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485   
         Q9NBA7_PLAFA   246 YEANYEDVIKKYKPADAKLDRIAYDWRLHGGVTPVKDQALCGSCWAFSSVGSVESQYAIRKKALFLFSEQELVDCSVKNNGCYGGYITNAFDDMIDLGGLCSQDDYPYVSNLPETCNLKRCNERYTIKSYVSIPDDKFKEALRYLGPISISIAASDDFAFYRGGFYDGECGAAPNHAVILVGYGMKDIYNEDTGRMEKFYYYIIKNSWGSDWGEGGYINLETDENGYKKTCSIGTEAYVPLLE 488
               SCOP domains d3bpma_ A: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 3bpmA00 A:8-250 Cysteine proteinases                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh..........ee.hhh.............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhh..ee...............hhhhh..ee...eeee....hhhhhhhhh..eeeee..hhhhhhh..............eeeeeeeeeeeeee......eeeeeeeeee...........eeeeee......hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bpm A   8 YEANYEDVIKKYKPADAKLDRIAYDWRLHGGVTPVKDQALCGSCWAFSSVGSVESQYAIRKKALFLFSEQELVDCSVKNNGCYGGYITNAFDDMIDLGGLCSQDDYPYVSNLPETCNLKRCNERYTIKSYVSIPDDKFKEALRYLGPISISIAASDDFAFYRGGFYDGECGAAPNHAVILVGYGMKDIYNEDTGRMEKFYYYIIKNSWGSDWGEGGYINLETDENGYKKTCSIGTEAYVPLLE 250
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain B from PDB  Type:PROTEIN  Length:232
 aligned with Q9NAW4_PLAFA | Q9NAW4 from UniProtKB/TrEMBL  Length:492

    Alignment length:241
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490 
         Q9NAW4_PLAFA   251 EANYEDVIKKYKPADAKLDRIAYDWRLHGGVTPVKDQALCGSCWAFSSVGSVESQYAIRKKALFLFSEQELVDCSVKNNGCYGGYITNAFDDMIDLGGLCSQDDYPYVSNLPETCNLKRCNERYTIKSYVSIPDDKFKEALRYLGPISISIAASDDFAFYRGGFYDGECGAAPNHAVILVGYGMKDIYNEDTGRMEKFYYYIIKNSWGSDWGEGGYINLETDENGYKKTCSIGTEAYVPLL 491
               SCOP domains d3bpmb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 3bpmB00 B:9-249 Cysteine proteinases                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..........ee.hhh.............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhh..ee...............hhhhh..ee...eeee.hhhhhhhhhhhh..eeeee..hhhhhhh..............eeeeeeeeeee.---------..eeeeeee...........eeeeee......hhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bpm B   9 EANYEDVIKKYKPADAKLDRIAYDWRLHGGVTPVKDQALCGSCWAFSSVGSVESQYAIRKKALFLFSEQELVDCSVKNNGCYGGYITNAFDDMIDLGGLCSQDDYPYVSNLPETCNLKRCNERYTIKSYVSIPDDKFKEALRYLGPISISIAASDDFAFYRGGFYDGECGAAPNHAVILVGYGMKD---------EKFYYYIIKNSWGSDWGEGGYINLETDENGYKKTCSIGTEAYVPLL 249
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     |   -     | 208       218       228       238       248 
                                                                                                                                                                                                                   194       204

Chain B from PDB  Type:PROTEIN  Length:232
 aligned with Q9NBA7_PLAFA | Q9NBA7 from UniProtKB/TrEMBL  Length:488

    Alignment length:241
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486 
         Q9NBA7_PLAFA   247 EANYEDVIKKYKPADAKLDRIAYDWRLHGGVTPVKDQALCGSCWAFSSVGSVESQYAIRKKALFLFSEQELVDCSVKNNGCYGGYITNAFDDMIDLGGLCSQDDYPYVSNLPETCNLKRCNERYTIKSYVSIPDDKFKEALRYLGPISISIAASDDFAFYRGGFYDGECGAAPNHAVILVGYGMKDIYNEDTGRMEKFYYYIIKNSWGSDWGEGGYINLETDENGYKKTCSIGTEAYVPLL 487
               SCOP domains d3bpmb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 3bpmB00 B:9-249 Cysteine proteinases                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..........ee.hhh.............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhh..ee...............hhhhh..ee...eeee.hhhhhhhhhhhh..eeeee..hhhhhhh..............eeeeeeeeeee.---------..eeeeeee...........eeeeee......hhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bpm B   9 EANYEDVIKKYKPADAKLDRIAYDWRLHGGVTPVKDQALCGSCWAFSSVGSVESQYAIRKKALFLFSEQELVDCSVKNNGCYGGYITNAFDDMIDLGGLCSQDDYPYVSNLPETCNLKRCNERYTIKSYVSIPDDKFKEALRYLGPISISIAASDDFAFYRGGFYDGECGAAPNHAVILVGYGMKD---------EKFYYYIIKNSWGSDWGEGGYINLETDENGYKKTCSIGTEAYVPLL 249
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     |   -     | 208       218       228       238       248 
                                                                                                                                                                                                                   194       204

Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3bpm C   1 xLLr   4
                            |  |
                            1-ACE
                               4-AR7

Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3bpm D   1 xLLr   4
                            |  |
                            |  |
                            1-ACE
                               4-AR7

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: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Papain-like (200)

Protein domain: automated matches (30)

Malaria parasite (Plasmodium falciparum) [TaxId: 5833] (2)

1a	d3bpma_	A:
1b	d3bpmb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Cathepsin B; Chain A (207)

Homologous Superfamily: Cysteine proteinases (207)

Plasmodium falciparum. Organism_taxid: 5833 (3)

1a	3bpmB00	B:9-249
1b	3bpmA00	A:8-250

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9NAW4_PLAFA | Q9NAW4)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	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.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B (Q9NBA7_PLAFA | Q9NBA7)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	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.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bpm)

Biological Units
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Access by PDB/NDB ID
	3bpm
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	Q9NAW4_PLAFA \| Q9NAW4
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	Q9NBA7_PLAFA \| Q9NBA7
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	3.4.22.-
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	Q9NAW4_PLAFA \| Q9NAW4
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	Q9NBA7_PLAFA \| Q9NBA7
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UniProtKB/Swiss-Prot
	Q9NBA7_PLAFA \| Q9NBA7	:	3bwk
UniProtKB/TrEMBL
	Q9NAW4_PLAFA \| Q9NAW4	:	3bwk

1aim	CRUZATIN (CYSTEINE PROTEASE) INHIBITED BY BENZOYL-TYROSINE- ALANINE-FLUOROMETHYLKETONE
1yvb	THE FALCIPAIN-2 (CYSTEINE PROTEASE) COMPLEXED WITH CYSTATIN
2ghu	THE FALCIPAIN-2 (CYSTEINE PROTEASE) COMPLEXED WITH IDOACETAMIDE
3bpf	THE FALCIPAIN-2 (CYSTEINE PROTEASE) COMPLEXED WITH E64

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (7, 7)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (5, 10)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File