2A3C - JenaLib

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Title :   CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 IN COMPLEX WITH PENTOXIFYLLINE

Authors :   F. V. Rao, O. A. Andersen, K. A. Vora, J. A. Demartino, D. M. F. Van Aalten

Date :   24 Jun 05 (Deposition) - 27 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.07

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

Keywords :   (Beta-Alpha)8 Barrel, Chitinase-Pentoxifylline Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. V. Rao, O. A. Andersen, K. A. Vora, J. A. Demartino, D. M. Van Aalten
Methylxanthine Drugs Are Chitinase Inhibitors: Investigation Of Inhibition And Binding Modes.
Chem. Biol. V. 12 973 2005
PubMed-ID: 16183021 | Reference-DOI: 10.1016/J.CHEMBIOL.2005.07.009
(for further references see the PDB file header)

Molecule 1 - CHITINASE
	Chains	:	A, B
	EC Number	:	3.2.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PLYSS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ASPERGILLUS FUMIGATUS
	Organism Taxid	:	5085
	Synonym	:	CHITINASE B1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	PNX	4	Ligand/Ion	3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE
2	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	PNX	2	Ligand/Ion	3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	PNX	2	Ligand/Ion	3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:126 , GLN A:414 , SER B:103	BINDING SITE FOR RESIDUE SO4 A 1001
02	AC2	SOFTWARE	THR A:149 , ASP A:150 , HOH A:1688 , HOH A:1820	BINDING SITE FOR RESIDUE SO4 A 1002
03	AC3	SOFTWARE	THR B:149 , ASP B:150 , HOH B:2598 , HOH B:2755	BINDING SITE FOR RESIDUE SO4 B 1003
04	AC4	SOFTWARE	ASN A:181 , ASP A:182 , HOH A:1729 , HOH A:1763	BINDING SITE FOR RESIDUE SO4 A 1004
05	AC5	SOFTWARE	ASN B:181 , ASP B:182	BINDING SITE FOR RESIDUE SO4 B 1005
06	AC6	SOFTWARE	HIS A:229 , LEU A:230 , LYS A:231 , ASP A:232 , HOH A:1630	BINDING SITE FOR RESIDUE SO4 A 1006
07	AC7	SOFTWARE	HIS B:229 , LEU B:230 , LYS B:231 , ASP B:232 , HOH B:2574 , HOH B:2665	BINDING SITE FOR RESIDUE SO4 B 1007
08	AC8	SOFTWARE	TRP A:52 , PHE A:76 , GLY A:136 , TRP A:137 , THR A:138 , ASP A:175 , GLU A:177 , MET A:243 , TYR A:245 , ASP A:246 , TRP A:384 , HOH A:1818 , HOH A:1819	BINDING SITE FOR RESIDUE PNX A 1434
09	AC9	SOFTWARE	GLN A:364 , TRP B:52 , PHE B:76 , GLY B:136 , TRP B:137 , THR B:138 , ASP B:175 , MET B:243 , TYR B:245 , ASP B:246 , TYR B:299 , TRP B:384 , HOH B:2492 , HOH B:2594	BINDING SITE FOR RESIDUE PNX B 2433
10	BC1	SOFTWARE	TRP A:137 , TYR A:178 , ASP A:246 , ALA A:248 , GLY A:249 , SER A:250 , PHE A:251 , ARG A:301	BINDING SITE FOR RESIDUE PNX A 1435
11	BC2	SOFTWARE	TRP B:137 , TYR B:178 , ASP B:246 , ALA B:248 , GLY B:249 , PHE B:251 , SER B:252 , ARG B:301	BINDING SITE FOR RESIDUE PNX B 2434

(no "SS Bond" information available for 2A3C)

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 2A3C)

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 2A3C)

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 d2a3ca1 A:39-298,A:361-433 Chitinase 1                                                                                                                                                                                                                              d2a3ca2 A:299-360 Chitinase 1                                 d2a3ca1 A:39-298,A:361-433 Chitinase 1                                    SCOP domains
               CATH domains 2a3cA01 A:39-297,A:361-433 Glycosidases                                                                                                                                                                                                                            2a3cA02 A:298-360  [code=3.10.50.10, no name defined]          2a3cA01 A:39-297,A:361-433 Glycosidases                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhhh....hhhhhhhhhh.eeeeeeeee......eee.hhhhhhh...............hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh...eeee........................hhhhh..hhhhhhhhhhhh..hhh.eeeeee.eeeee.....................eee.hhh.....eeeeehhhheeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhhhhh.hhhhh.............hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------CHITINASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a3c 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:394
 aligned with CHIB1_ASPFM | Q873X9 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:394
                                    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 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQ 432
               SCOP domains d2a3cb1 B:39-298,B:361-432 Chitinase 1                                                                                                                                                                                                                              d2a3cb2 B:299-360 Chitinase 1                                 d2a3cb1 B:39-298,B:361-432 Chitinase 1                                   SCOP domains
               CATH domains 2a3cB01 B:39-297,B:361-432 Glycosidases                                                                                                                                                                                                                            2a3cB02 B:298-360  [code=3.10.50.10, no name defined]          2a3cB01 B:39-297,B:361-432 Glycosidases                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhhh....hhhhhhhhhh.eeeeeeeee......eee.hhhhhh................hhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhh.eeee........................hhhhh..hhhhhhhhhhhh..hhh.eeeeee.eeeee.....................eee.hhh.....eeeeehhhheeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhhhhhhhhhhh.............hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------CHITINASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a3c B  39 ASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQ 432
                                    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

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	d2a3ca2	A:299-360
1b	d2a3cb2	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	d2a3ca1	A:39-298,A:361-433
2b	d2a3cb1	B:39-298,B:361-432

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. (5)

1a	2a3cA01	A:39-297,A:361-433
1b	2a3cB01	B:39-297,B:361-432

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. (5)

2a	2a3cA02	A:298-360
2b	2a3cB02	B:298-360

(no "Pfam Domain" information available for 2A3C)

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

1w9p	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1
1w9u	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 IN COMPLEX WITH ARGADIN
1w9v	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 IN COMPLEX WITH ARGIFIN
2a3a	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 IN COMPLEX WITH THEOPHYLLINE
2a3b	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 IN COMPLEX WITH CAFFEINE
2a3e	CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS CHITINASE B1 IN COMPLEX WITH ALLOSAMIDIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

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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