3HY9 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF ADAMTS-5 IN COMPLEX WITH AN AMINO-2-INDANOL COMPOUND

Authors :   H. -S. Shieh, J. M. Williams, N. Caspers, K. J. Mathis, M. D. Tortorella, A. Tomasselli

Date :   22 Jun 09 (Deposition) - 07 Jul 09 (Release) - 15 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.02

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

Keywords :   Alpha/Beta Structure, Central Five Stranded Beta-Sheet, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. Tortorella, A. G. Tomasselli, K. J. Mathis, M. E. Schnute, S. S. Woodard, G. Munie, J. M. Williams, N. Caspers, A. J. Wittwer, A. M. Malfait, H. S. Shieh
Structural And Inhibition Analysis Reveals The Mechanism Of Selectivity Of A Series Of Aggrecanase Inhibitors
J. Biol. Chem. V. 284 24185 2009
PubMed-ID: 19586907 | Reference-DOI: 10.1074/JBC.M109.029116
(for further references see the PDB file header)

Molecule 1 - CATALYTIC DOMAIN OF ADAMTS-5
	Chains	:	A, B
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPHA79257
	Expression System Strain	:	MON208
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN (UNP RESIDUES 262 TO 480)
	Gene	:	ADAMTS-5
	Mutation	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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 (3, 10)

No.	Name	Count	Type	Full Name
1	098	2	Ligand/Ion	(3R)-N~2~-(CYCLOPROPYLMETHYL)-N~1~-HYDROXY-3-(3-HYDROXYBENZYL)-N~4~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]-L-ASPARTAMIDE
2	CA	6	Ligand/Ion	CALCIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	098	1	Ligand/Ion	(3R)-N~2~-(CYCLOPROPYLMETHYL)-N~1~-HYDROXY-3-(3-HYDROXYBENZYL)-N~4~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]-L-ASPARTAMIDE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	098	1	Ligand/Ion	(3R)-N~2~-(CYCLOPROPYLMETHYL)-N~1~-HYDROXY-3-(3-HYDROXYBENZYL)-N~4~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]-L-ASPARTAMIDE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:410 , HIS A:414 , HIS A:420 , 098 A:801	BINDING SITE FOR RESIDUE ZN A 901
02	AC2	SOFTWARE	GLU A:270 , ASP A:353 , ASP A:360 , CYS A:471 , ASP A:474 , HOH A:5001	BINDING SITE FOR RESIDUE CA A 902
03	AC3	SOFTWARE	GLU A:270 , ASP A:353 , ASP A:474 , HOH A:5026 , HOH A:5033	BINDING SITE FOR RESIDUE CA A 903
04	AC4	SOFTWARE	ASP A:369 , LEU A:370 , CYS A:376 , THR A:378 , GLU A:398 , HOH A:5029	BINDING SITE FOR RESIDUE CA A 904
05	AC5	SOFTWARE	HIS A:373 , ASP A:377 , THR A:378 , LEU A:379 , GLY A:380 , THR A:407 , HIS A:410 , GLU A:411 , HIS A:414 , HIS A:420 , LEU A:438 , SER A:440 , SER A:441 , ILE A:442 , LEU A:443 , ZN A:901 , HOH A:5013 , HOH A:5037 , HOH A:5102 , HOH A:5190	BINDING SITE FOR RESIDUE 098 A 801
06	AC6	SOFTWARE	HIS B:410 , HIS B:414 , HIS B:420 , 098 B:801	BINDING SITE FOR RESIDUE ZN B 901
07	AC7	SOFTWARE	GLU B:270 , ASP B:353 , ASP B:360 , CYS B:471 , ASP B:474 , HOH B:6012	BINDING SITE FOR RESIDUE CA B 902
08	AC8	SOFTWARE	GLU B:270 , ASP B:353 , ASP B:474 , HOH B:6097 , HOH B:6180	BINDING SITE FOR RESIDUE CA B 903
09	AC9	SOFTWARE	ASP B:369 , LEU B:370 , CYS B:376 , THR B:378 , GLU B:398 , HOH B:6003	BINDING SITE FOR RESIDUE CA B 904
10	BC1	SOFTWARE	ASP B:377 , THR B:378 , LEU B:379 , GLY B:380 , THR B:407 , HIS B:410 , GLU B:411 , HIS B:414 , HIS B:420 , LEU B:438 , SER B:440 , SER B:441 , ILE B:442 , LEU B:443 , ZN B:901 , HOH B:6021 , HOH B:6063 , HOH B:6081	BINDING SITE FOR RESIDUE 098 B 801

Asymmetric Unit

No.	Residues
1	A:342	-	A:394
2	A:371	-	A:376
3	A:388	-	A:471
4	A:426	-	A:455
5	B:342	-	B:394
6	B:371	-	B:376
7	B:388	-	B:471
8	B:426	-	B:455

(no "Cis Peptide Bond" information available for 3HY9)

(no "SAP(SNP)/Variant" information available for 3HY9)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	ATS5_HUMAN	267-476	2	A:267-476 B:267-476
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	ATS5_HUMAN	407-416	2	A:407-416 B:407-416

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	ATS5_HUMAN	267-476	1	A:267-476 -
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	ATS5_HUMAN	407-416	1	A:407-416 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	ATS5_HUMAN	267-476	1	- B:267-476
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	ATS5_HUMAN	407-416	1	- B:407-416

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000284987	1	ENSE00001017391	chr21:28338832-28337607	1226	ATS5_HUMAN	1-368	368	2	A:264-368 B:261-368	105 108
1.2	ENST00000284987	2	ENSE00001017390	chr21:28327190-28327058	133	ATS5_HUMAN	369-413	45	2	A:369-413 B:369-413	45 45
1.3	ENST00000284987	3	ENSE00001017386	chr21:28315866-28315699	168	ATS5_HUMAN	413-469	57	2	A:413-469 B:413-469	57 57
1.4	ENST00000284987	4	ENSE00001017392	chr21:28307068-28306785	284	ATS5_HUMAN	469-563	95	2	A:469-480 B:469-480	12 12
1.5	ENST00000284987	5	ENSE00001017389	chr21:28305363-28305180	184	ATS5_HUMAN	564-625	62	0	-	-
1.6	ENST00000284987	6	ENSE00001017388	chr21:28304498-28304323	176	ATS5_HUMAN	625-683	59	0	-	-
1.7	ENST00000284987	7	ENSE00001017393	chr21:28302380-28302205	176	ATS5_HUMAN	684-742	59	0	-	-
1.8	ENST00000284987	8	ENSE00001017387	chr21:28296939-28290231	6709	ATS5_HUMAN	742-930	189	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:217
 aligned with ATS5_HUMAN | Q9UNA0 from UniProtKB/Swiss-Prot  Length:930

    Alignment length:217
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       
           ATS5_HUMAN   264 SRARQVELLLVADASMARLYGRGLQHYLLTLASIANRLYSHASIENHIRLAVVKVVVLGDKDKSLEVSKNAATTLKNFCKWQHQHNQLGDDHEEHYDAAILFTREDLCGHHSCDTLGMADVGTICSPERSCAVIEDDGLHAAFTVAHEIGHLLGLSHDDSKFCEETFGSTEDKRLMSSILTSIDASKPWSKCTSATITEFLDDGHGNCLLDLPRKQI 480
               SCOP domains d3hy9a_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee............hhhhhhhhhhhhhhhhh...........eeeeee.............eee......hhhh.eeeee....hhhhhhhhhhhhhh......hhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ADAM_MEPRO  PDB: A:267-476 UniProt: 267-476                                                                                                                                                                       ---- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:264-368 UniProt: 1-368 [INCOMPLETE]                                                     Exon 1.2  PDB: A:369-413 UniProt: 369-413    -------------------------------------------------------Exon 1.4     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:413-469 UniProt: 413-469                ----------- Transcript 1 (2)
                 3hy9 A 264 SRARQVELLLVADASMARKYGRGLQHYLLTLASIANRLYSHASIENHIRLAVVKVVVLGDKDKSLEVSKNAATTLKNFCKWQHQHNQLGDDHEEHYDAAILFTREDLCGHHSCDTLGMADVGTICSPERSCAVIEDDGLHAAFTVAHEIGHLLGLSHDDSKFCEETFGSTEDKRLMSSILTSIDASKPWSKCTSATITEFLDDGHGNCLLDLPRKQI 480
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with ATS5_HUMAN | Q9UNA0 from UniProtKB/Swiss-Prot  Length:930

    Alignment length:220
                                   270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480
           ATS5_HUMAN   261 RSISRARQVELLLVADASMARLYGRGLQHYLLTLASIANRLYSHASIENHIRLAVVKVVVLGDKDKSLEVSKNAATTLKNFCKWQHQHNQLGDDHEEHYDAAILFTREDLCGHHSCDTLGMADVGTICSPERSCAVIEDDGLHAAFTVAHEIGHLLGLSHDDSKFCEETFGSTEDKRLMSSILTSIDASKPWSKCTSATITEFLDDGHGNCLLDLPRKQI 480
               SCOP domains d3hy9b_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee............hhhhhhhhhhhhhhhhh...........eeeeee.............eee......hhhh.eeeee....hhhhhhhhhhhhhh......hhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------ADAM_MEPRO  PDB: B:267-476 UniProt: 267-476                                                                                                                                                                       ---- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: B:261-368 UniProt: 1-368 [INCOMPLETE]                                                        Exon 1.2  PDB: B:369-413 UniProt: 369-413    -------------------------------------------------------Exon 1.4     Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: B:413-469 UniProt: 413-469                ----------- Transcript 1 (2)
                 3hy9 B 261 ASISRARQVELLLVADASMARKYGRGLQHYLLTLASIANRLYSHASIENHIRLAVVKVVVLGDKDKSLEVSKNAATTLKNFCKWQHQHNQLGDDHEEHYDAAILFTREDLCGHHSCDTLGMADVGTICSPERSCAVIEDDGLHAAFTVAHEIGHLLGLSHDDSKFCEETFGSTEDKRLMSSILTSIDASKPWSKCTSATITEFLDDGHGNCLLDLPRKQI 480
                                   270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Zincin-like (701)

Superfamily: Metalloproteases (zincins), catalytic domain (647)

Family: automated matches (37)

Protein domain: automated matches (37)

Human (Homo sapiens) [TaxId: 9606] (22)

1a	d3hy9a_	A:
1b	d3hy9b_	B:

(no "CATH Domain" information available for 3HY9)

(no "Pfam Domain" information available for 3HY9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ATS5_HUMAN | Q9UNA0)

molecular function
	GO:0050840	extracellular matrix binding	Interacting selectively and non-covalently with a component of the extracellular matrix.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	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:0005178	integrin binding	Interacting selectively and non-covalently with an integrin.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	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.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0036066	protein O-linked fucosylation	The process of transferring a fucosyl group to a serine or threonine residues in a protein acceptor molecule, to form an O-linked protein-sugar linkage.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hy9)

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Access by PDB/NDB ID
	3hy9
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	3.4.24.-
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UniProtKB/Swiss-Prot
	ATS5_HUMAN \| Q9UNA0	:	2rjq 3b8z 3hy7 3hyg 3ljt

3b8z	THE SAME PROTEIN COMPLEXED WITH DIFFERENT INHIBITOR.
3hy7	THE SAME PROTEIN COMPLEXED WITH DIFFERENT INHIBITOR.
3hyg	THE SAME PROTEIN COMPLEXED WITH DIFFERENT INHIBITOR.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (4, 8)

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SCOP Domains (1, 2)

CATH Domains (0, 0)

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Gene Ontology (19, 19)

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