1W9U - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   SPECIFICITY AND AFFNITY OF NATURAL PRODUCT CYCLOPENTAPEPTIDE INHIBITOR ARGADIN AGAINST ASPERGILLUS FUMIGATUS CHITINASE

Authors :   F. V. Rao, D. R. Houston, R. G. Boot, J. M. F. G. Aerts, M. Hodkinson, D. J. A K. Shiomi, S. Omura, D. M. F. Van Aalten

Date :   19 Oct 04 (Deposition) - 17 Nov 04 (Release) - 05 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Chitinase, Argadin, Cyclopentapeptide Inhibitors, Chitinase Inhibitors, Glycosidase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. V. Rao, D. R. Houston, R. G. Boot, J. M. F. G. Aerts, M. Hodkinson, D. J. Adams, K. Shiomi, S. Omura, D. M. F. Van Aalten
Specificity And Affinity Of Natural Product Cyclopentapeptide Inhibitors Against Aspergillus Fumigatus, Human And Bacterial Chitinases
Chem. Biol. V. 12 65 2005
PubMed-ID: 15664516 | Reference-DOI: 10.1016/J.CHEMBIOL.2004.10.013

Molecule 1 - CHITINASE
	Atcc	:	13073
	Chains	:	A, B
	EC Number	:	3.2.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Organism Scientific	:	ASPERGILLUS FUMIGATUS
	Organism Taxid	:	746128

Molecule 2 - ARGADIN
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	CLONOSTACHYS
	Organism Taxid	:	110564
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	0AR	2	Mod. Amino Acid	N-[N-[(4S)-4-AZANYL-5-HYDROXY-5-OXO-PENTYL]CARBAMIMIDOYL]ETHANAMIDE
2	DPR	2	Mod. Amino Acid	D-PROLINE
3	HSE	2	Mod. Amino Acid	L-HOMOSERINE
4	SO4	7	Ligand/Ion	SULFATE ION
5	UN1	2	Mod. Amino Acid	2-AMINOHEXANEDIOIC ACID

Biological Unit 1 (5, 8)

No.	Name	Count	Type	Full Name
1	0AR	1	Mod. Amino Acid	N-[N-[(4S)-4-AZANYL-5-HYDROXY-5-OXO-PENTYL]CARBAMIMIDOYL]ETHANAMIDE
2	DPR	1	Mod. Amino Acid	D-PROLINE
3	HSE	1	Mod. Amino Acid	L-HOMOSERINE
4	SO4	4	Ligand/Ion	SULFATE ION
5	UN1	1	Mod. Amino Acid	2-AMINOHEXANEDIOIC ACID

Biological Unit 2 (5, 7)

No.	Name	Count	Type	Full Name
1	0AR	1	Mod. Amino Acid	N-[N-[(4S)-4-AZANYL-5-HYDROXY-5-OXO-PENTYL]CARBAMIMIDOYL]ETHANAMIDE
2	DPR	1	Mod. Amino Acid	D-PROLINE
3	HSE	1	Mod. Amino Acid	L-HOMOSERINE
4	SO4	3	Ligand/Ion	SULFATE ION
5	UN1	1	Mod. Amino Acid	2-AMINOHEXANEDIOIC ACID

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:229 , LEU A:230 , LYS A:231 , ASP A:232 , HOH A:2403 , HOH A:2675	BINDING SITE FOR RESIDUE SO4 A 1439
2	AC2	SOFTWARE	ASN A:181 , ASP A:182 , HOH A:2676 , HOH A:2677	BINDING SITE FOR RESIDUE SO4 A 1440
3	AC3	SOFTWARE	THR A:149 , ASP A:150 , HOH A:2678 , HOH A:2679 , HOH A:2680	BINDING SITE FOR RESIDUE SO4 A 1441
4	AC4	SOFTWARE	HOH A:2161 , HOH A:2681 , HOH A:2682 , HOH A:2683 , ARG B:283 , ALA B:289 , HOH B:2396	BINDING SITE FOR RESIDUE SO4 A 1442
5	AC5	SOFTWARE	SER B:148 , THR B:149 , ASP B:150 , HOH B:2595 , HOH B:2596 , HOH B:2597	BINDING SITE FOR RESIDUE SO4 B 1438
6	AC6	SOFTWARE	HIS B:229 , LEU B:230 , LYS B:231 , ASP B:232 , HOH B:2598 , HOH B:2599	BINDING SITE FOR RESIDUE SO4 B 1439
7	AC7	SOFTWARE	ASN B:181 , ASP B:182 , HOH B:2600 , HOH B:2601	BINDING SITE FOR RESIDUE SO4 B 1440
8	AC8	SOFTWARE	TYR A:48 , TRP A:137 , ASP A:175 , GLU A:177 , TYR A:245 , ASP A:246 , PHE A:251 , TYR A:299 , ARG A:301 , VAL A:325 , TRP A:384 , HOH C:2667 , HOH C:2669 , HOH C:2670 , HOH C:2671 , HOH C:2672 , HOH C:2673 , HOH C:2674	BINDING SITE FOR CHAIN C OF ARGADIN
9	AC9	SOFTWARE	TYR B:48 , TRP B:137 , ASP B:175 , GLU B:177 , TYR B:245 , ASP B:246 , PHE B:251 , TYR B:299 , ARG B:301 , GLU B:322 , VAL B:325 , TRP B:384 , HOH B:2341 , HOH D:2585 , HOH D:2586 , HOH D:2589 , HOH D:2591 , HOH D:2592	BINDING SITE FOR CHAIN D OF ARGADIN

(no "SS Bond" information available for 1W9U)

Asymmetric Unit

No.	Residues
1	Ala A:75	-	Phe A:76
2	Glu A:177	-	Tyr A:178
3	Leu A:331	-	Pro A:332
4	Trp A:384	-	Asp A:385
5	Ala B:75	-	Phe B:76
6	Glu B:177	-	Tyr B:178
7	Leu B:331	-	Pro B:332
8	Trp B:384	-	Asp B:385

(no "SAP(SNP)/Variant" information available for 1W9U)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIB1_ASPFM	169-177	2	A:169-177 B:169-177

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIB1_ASPFM	169-177	1	A:169-177 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIB1_ASPFM	169-177	1	- B:169-177

(no "Exon" information available for 1W9U)

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:395
 aligned with CHIB1_ASPFM | Q873X9 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:395
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     
         CHIB1_ASPFM     39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT  433
               SCOP domains d1w9ua1 A:39-298,A:361-433 Chitinase 1                                                                                                                                                                                                                              d1w9ua2 A:299-360 Chitinase 1                                 d1w9ua1 A:39-298,A:361-433 Chitinase 1                                    SCOP domains
               CATH domains 1w9uA01 A:39-297,A:361-433 Glycosidases                                                                                                                                                                                                                            1w9uA02 A:298-360  [code=3.10.50.10, no name defined]          1w9uA01 A:39-297,A:361-433 Glycosidases                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhhh....hhhhhhhhhh.eeeeeeeee..........hhhhhhh...............hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh...eeee........................hhhhh..hhhhhhhhhhhh..hhh.eeeeee.eeeee.....................eee.hhh.....eeeeehhhheeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhhhhh.hhhh..............hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------CHITINASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1w9u A   39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT  433
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428

Chain B from PDB  Type:PROTEIN  Length:395
 aligned with CHIB1_ASPFM | Q873X9 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:395
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     
         CHIB1_ASPFM     39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT  433
               SCOP domains d1w9ub1 B:39-298,B:361-433 Chitinase 1                                                                                                                                                                                                                              d1w9ub2 B:299-360 Chitinase 1                                 d1w9ub1 B:39-298,B:361-433 Chitinase 1                                    SCOP domains
               CATH domains 1w9uB01 B:39-297,B:361-433 Glycosidases                                                                                                                                                                                                                            1w9uB02 B:298-360  [code=3.10.50.10, no name defined]          1w9uB01 B:39-297,B:361-433 Glycosidases                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhhh....hhhhhhhhhh.eeeeeeeee..........hhhhhh................hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh...eeee........................hhhhh..hhhhhhhhhhhh..hhh.eeeeee.eeeee.....................eee.hhh.....eeeeehhhheeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhhhhhhhhhh..............hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------CHITINASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1w9u B   39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT  433
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428

Chain C from PDB  Type:PROTEIN  Length:5
                                      
               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
                1w9u C 1434 xxxHx 1438
                            ||| |
                         1434-0AR
                          1435-DPR
                           1436-HSE
                             1438-UN1

Chain D from PDB  Type:PROTEIN  Length:5
                                      
               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
                1w9u D 1434 xxxHx 1438
                            ||| |
                            ||| |
                         1434-0AR
                          1435-DPR
                           1436-HSE
                             1438-UN1

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: FKBP-like (309)

Superfamily: Chitinase insertion domain (107)

Family: Chitinase insertion domain (107)

Protein domain: Chitinase 1 (18)

Aspergillus fumigatus [TaxId: 5085] (14)

1a	d1w9ua2	A:299-360
1b	d1w9ub2	B:299-360

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: Type II chitinase (131)

Protein domain: Chitinase 1 (18)

Aspergillus fumigatus [TaxId: 5085] (14)

2a	d1w9ua1	A:39-298,A:361-433
2b	d1w9ub1	B:39-298,B:361-433

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Aspergillus fumigatus. Organism_taxid: 5085. (8)

1a	1w9uA01	A:39-297,A:361-433
1b	1w9uB01	B:39-297,B:361-433

Architecture: Roll (3276)

Topology: Chitinase A; domain 3 (225)

Homologous Superfamily: [code=3.10.50.10, no name defined] (121)

Aspergillus fumigatus. Organism_taxid: 5085. (8)

2a	1w9uA02	A:298-360
2b	1w9uB02	B:298-360

(no "Pfam Domain" information available for 1W9U)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHIB1_ASPFM | Q873X9)

molecular function
	GO:0004568	chitinase activity	Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006032	chitin catabolic process	The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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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	Cis Peptide Bonds
		Ala A:75 - Phe A:76	[ RasMol ]
		Ala B:75 - Phe B:76	[ RasMol ]
		Glu A:177 - Tyr A:178	[ RasMol ]
		Glu B:177 - Tyr B:178	[ RasMol ]
		Leu A:331 - Pro A:332	[ RasMol ]
		Leu B:331 - Pro B:332	[ RasMol ]
		Trp A:384 - Asp A:385	[ RasMol ]
		Trp B:384 - Asp B:385	[ RasMol ]

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	1w9u
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	3.2.1.14
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	CHIB1_ASPFM \| Q873X9	:	1w9p 1w9v 1wno 2a3a 2a3b 2a3c 2a3e 2iuz 3ch9 3chc 3chd 3che 3chf

1w9p	SPECIFICITY AND AFFINITY OF NATURAL PRODUCT CYCLOPENTAPEPTIDE INHIBITORS AGAINST ASPERGILLUS FUMIGATUS, HUMAN AND BACTERIAL CHITINASE
1w9v	SPECIFICITY AND AFFINITY OF NATURAL PRODUCT CYCLOPENTAPEPTIDE ARGIFIN AGAINST ASPERGILLUS FUMIGATUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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Related Entries Specified in the PDB File