1HKK - JenaLib

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Title :   HIGH RESOULTION CRYSTAL STRUCTURE OF HUMAN CHITINASE IN COMPLEX WITH ALLOSAMIDIN

Authors :   F. V. Rao, D. R. Houston, R. G. Boot, J. M. F. G. Aerts, S. Sakuda, D. M. F. Van Aalten

Date :   10 Mar 03 (Deposition) - 11 Mar 04 (Release) - 12 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)

Keywords :   Human Chitinase, Hydrolase, Chitin Degradation, Allosamidin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. V. Rao, D. R. Houston, R. G. Boot, J. M. F. G. Aerts, S. Sakuda, D. M. F. Van Aalten
Crystal Structures Of Allosamidin Derivatives In Complex With Human Macrophage Chitinase.
J. Biol. Chem. V. 278 20110 2003
PubMed-ID: 12639956 | Reference-DOI: 10.1074/JBC.M300362200

Molecule 1 - CHITOTRIOSIDASE-1
	Cell	:	MACROPHAGES
	Chains	:	A
	EC Number	:	3.2.1.14
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	ALLOSAMIDIN
	Synonym	:	CHITINASE-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	AMI	2	Ligand/Ion	ALLOSAMIZOLINE
2	NAA	4	Ligand/Ion	N-ACETYL-D-ALLOSAMINE
3	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	AMI	2	Ligand/Ion	ALLOSAMIZOLINE
2	NAA	4	Ligand/Ion	N-ACETYL-D-ALLOSAMINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:215 , GLU A:219 , HOH A:2246 , HOH A:2247 , HOH A:2248	BINDING SITE FOR RESIDUE ZN A1392
2	AC2	SOFTWARE	HIS A:64 , ASP A:108 , ASN A:115 , HOH A:2249	BINDING SITE FOR RESIDUE ZN A1393
3	AC3	SOFTWARE	HOH A:2023 , HOH A:2250 , HOH A:2251 , HOH A:2252 , HOH A:2253	BINDING SITE FOR RESIDUE ZN A1394
4	AC4	SOFTWARE	TYR A:27 , TRP A:31 , PHE A:58 , TRP A:99 , ASN A:100 , ASP A:138 , GLU A:140 , ALA A:183 , MET A:210 , TYR A:212 , ASP A:213 , TYR A:267 , GLU A:297 , MET A:300 , MET A:356 , TRP A:358 , ARG A:374 , GLN A:379 , NAA A:1389 , NAA A:1390 , HOH A:2237 , HOH A:2238 , HOH A:2239 , HOH A:2240 , HOH A:2241 , HOH A:2242	BINDING SITE FOR CHAIN A OF RESIDUES 1386 TO 1388
5	AC5	SOFTWARE	TRP A:99 , GLU A:140 , TYR A:141 , GLN A:145 , ALA A:186 , GLY A:187 , TYR A:190 , ASP A:213 , TRP A:218 , ARG A:269 , GLU A:297 , ASN A:371 , GLY A:373 , NAA A:1387 , AMI A:1388 , HOH A:2142 , HOH A:2144 , HOH A:2243 , HOH A:2244 , HOH A:2245	BINDING SITE FOR CHAIN A OF RESIDUES 1389 TO 1391

Asymmetric Unit

No.	Residues
1	A:26	-	A:51
2	A:307	-	A:370

Asymmetric Unit

No.	Residues
1	Ala A:57	-	Phe A:58
2	Glu A:140	-	Tyr A:141
3	Trp A:358	-	Ala A:359

Asymmetric Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049190	R	40	H	CHIT1_HUMAN	Polymorphism	35920428	A	R	40	H
2	UniProt	VAR_065914	E	74	K	CHIT1_HUMAN	Polymorphism	137852607	A	E	74	K
3	UniProt	VAR_022138	G	102	S	CHIT1_HUMAN	Polymorphism	2297950	A	G	102	S
4	UniProt	VAR_049191	Q	171	H	CHIT1_HUMAN	Polymorphism	12562058	A	Q	171	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049190	R	40	H	CHIT1_HUMAN	Polymorphism	35920428	A	R	40	H
2	UniProt	VAR_065914	E	74	K	CHIT1_HUMAN	Polymorphism	137852607	A	E	74	K
3	UniProt	VAR_022138	G	102	S	CHIT1_HUMAN	Polymorphism	2297950	A	G	102	S
4	UniProt	VAR_049191	Q	171	H	CHIT1_HUMAN	Polymorphism	12562058	A	Q	171	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIT1_HUMAN	132-140	1	A:132-140

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.	CHIT1_HUMAN	132-140	1	A:132-140

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.8a	ENST00000367229	8a	ENSE00001443882	chr1:203198799-203198740	60	CHIT1_HUMAN	1-9	9	0	-	-
1.9	ENST00000367229	9	ENSE00001608418	chr1:203197690-203197661	30	CHIT1_HUMAN	9-19	11	0	-	-
1.10	ENST00000367229	10	ENSE00001767547	chr1:203194998-203194797	202	CHIT1_HUMAN	19-86	68	1	A:22-86	65
1.11	ENST00000367229	11	ENSE00001697138	chr1:203194232-203194176	57	CHIT1_HUMAN	86-105	20	1	A:86-105	20
1.12b	ENST00000367229	12b	ENSE00001666970	chr1:203192788-203192623	166	CHIT1_HUMAN	105-160	56	1	A:105-160	56
1.13	ENST00000367229	13	ENSE00000907172	chr1:203192387-203192263	125	CHIT1_HUMAN	161-202	42	1	A:161-202	42
1.14a	ENST00000367229	14a	ENSE00001687399	chr1:203191453-203191330	124	CHIT1_HUMAN	202-243	42	1	A:202-243	42
1.15a	ENST00000367229	15a	ENSE00000907170	chr1:203188977-203188792	186	CHIT1_HUMAN	244-305	62	1	A:244-305	62
1.16	ENST00000367229	16	ENSE00000907169	chr1:203188457-203188344	114	CHIT1_HUMAN	306-343	38	1	A:306-343	38
1.17c	ENST00000367229	17c	ENSE00001130578	chr1:203186993-203186867	127	CHIT1_HUMAN	344-386	43	1	A:344-385	42
1.19c	ENST00000367229	19c	ENSE00001443883	chr1:203186261-203185207	1055	CHIT1_HUMAN	386-466	81	0	-	-

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:364
 aligned with CHIT1_HUMAN | Q13231 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:364
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381    
          CHIT1_HUMAN    22 AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEESGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQEL 385
               SCOP domains d1hkka1 A:22-266,A:335-385 Chitotriosidase                                                                                                                                                                                                           d1hkka2 A:267-334 Chitotriosidase                                   d1hkka1 A:22-266,A:335-385 Chitotriosidase          SCOP domains
               CATH domains 1hkkA01 A:22-266,A:335-385 Glycosidases                                                                                                                                                                                                              1hkkA02 A:267-334  [code=3.10.50.10, no name defined]               1hkkA01 A:22-266,A:335-385 Glycosidases             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhh.hhhhh......eeeeeeeeee.........hhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhh.eeeee........................hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.eeeeeee...........eeee...........eeehhhhh.....eeeee....eeeeee..eeee..hhhhhhhhhhhhhhh...eeeeehhhhh...........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------H---------------------------------K---------------------------S--------------------------------------------------------------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------CHITINASE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:22-86 UniProt: 19-86 [INCOMPLETE]              ------------------Exon 1.12b  PDB: A:105-160 UniProt: 105-160             Exon 1.13  PDB: A:161-202 UniProt: 161-202-----------------------------------------Exon 1.15a  PDB: A:244-305 UniProt: 244-305                   Exon 1.16  PDB: A:306-343             Exon 1.17c  PDB: A:344-385 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.11           ------------------------------------------------------------------------------------------------Exon 1.14a  PDB: A:202-243                ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1hkk A  22 AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEQSGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQEL 385
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381

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(

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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: Chitotriosidase (10)

Human (Homo sapiens) [TaxId: 9606] (10)

d1hkka2

A:267-334

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: Chitotriosidase (10)

Human (Homo sapiens) [TaxId: 9606] (10)

d1hkka1

A:22-266,A:335-385

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Human (Homo sapiens) (94)

1hkkA01

A:22-266,A:335-385

Architecture: Roll (3276)

Topology: Chitinase A; domain 3 (225)

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

Human (Homo sapiens) (19)

1hkkA02

A:267-334

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

Asymmetric Unit(hide GO term definitions)

Chain A (CHIT1_HUMAN | Q13231)

molecular function
	GO:0008061	chitin binding	Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
	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:0008843	endochitinase activity	Catalysis of the hydrolysis of nonterminal (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins. Typically, endochitinases cleave randomly within the chitin chain.
	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:0006030	chitin metabolic process	The chemical reactions and pathways involving chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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.
	GO:0009617	response to bacterium	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:57 - Phe A:58	[ RasMol ]
		Glu A:140 - Tyr A:141	[ RasMol ]
		Trp A:358 - Ala A:359	[ RasMol ]

Biological Unit
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	1hkk
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	CHIT1_HUMAN \| Q13231
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	3.2.1.14
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1guv	STRUCTURE OF HUMAN CHITOTRIOSIDASE
1hki	CRYSTAL STRUCTURE OF HUMAN CHITINASE IN COMPLEX WITH GLUCOALLOSAMIDIN B
1hkj	CRYSTAL STRUCTURE OF HUMAN CHITINASE IN COMPLEX WITH METHYLALLOSAMIDIN
1hkm	HIGH RESOULTION CRYSTAL STRUCTURE OF HUMAN CHITINASE IN COMPLEX WITH DEMETHYLALLOSAMIDIN
1lg1	CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE IN COMPLEX WITHCHITOBIOSE
1lg2	CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE IN COMPLEX WITHETHYLENE GLYCOL
1lq0	CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE AT 2.2 ANGSTROMRESOLUTION
1waw	SPECIFICITY AND AFFNITY OF NATURAL PRODUCT CYCLOPENTAPEPTIDE INHIBITOR ARGADIN AGAINST HUMAN CHITINASE
1wb0	SPECIFICITY AND AFFINITY OF NATURAL PRODUCT CYCLOPENTAPEPTIDE INHIBITOR ARGIFIN AGAINST HUMAN CHITINAES

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (1, 1)

Exons (8, 8)

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SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

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