2OY2 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN MMP-8 IN COMPLEX WITH PEPTIDE IAG

Authors :   V. Calderone, I. Bertini, M. Fragai, C. Luchinat, M. Maletta, K. J. Yeo

Date :   21 Feb 07 (Deposition) - 06 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,F,W,Y
Biol. Unit 1: A,W  (1x)
Biol. Unit 2: F,Y  (1x)

Keywords :   Mmp-8, Matrix Metalloproteinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Bertini, V. Calderone, M. Fragai, C. Luchinat, M. Maletta, K. J. Yeo
Snapshots Of The Reaction Mechanism Of Matrix Metalloproteinases.
Angew. Chem. Int. Ed. Engl. V. 45 7952 2006
PubMed-ID: 17096442 | Reference-DOI: 10.1002/ANIE.200603100
(for further references see the PDB file header)

Molecule 1 - NEUTROPHIL COLLAGENASE
	Chains	:	A, F
	EC Number	:	3.4.24.34
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	MMP8, CLG1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MATRIX METALLOPROTEINASE-8, MMP-8, PMNL COLLAGENASE, PMNL-CL

Molecule 2 - ILE-ALA-GLY PEPTIDE
	Chains	:	W, Y
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	F	W	Y
Biological Unit 1 (1x)	:	A		W
Biological Unit 2 (1x)	:		F		Y

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:137 , GLY A:169 , GLY A:171 , ASP A:173 , HOH A:1015 , HOH A:1027	BINDING SITE FOR RESIDUE CA A 996
2	AC2	SOFTWARE	ASP A:154 , GLY A:155 , ASN A:157 , ILE A:159 , ASP A:177 , GLU A:180	BINDING SITE FOR RESIDUE CA A 997
3	AC3	SOFTWARE	HIS A:147 , ASP A:149 , HIS A:162 , HIS A:175	BINDING SITE FOR RESIDUE ZN A 998
4	AC4	SOFTWARE	HIS A:197 , HIS A:201 , HIS A:207 , HOH A:1059 , HOH A:1183	BINDING SITE FOR RESIDUE ZN A 999
5	AC5	SOFTWARE	ASP F:137 , GLY F:169 , GLY F:171 , ASP F:173 , HOH F:1010 , HOH F:1027	BINDING SITE FOR RESIDUE CA F 996
6	AC6	SOFTWARE	ASP F:154 , GLY F:155 , ASN F:157 , ILE F:159 , ASP F:177 , GLU F:180	BINDING SITE FOR RESIDUE CA F 997
7	AC7	SOFTWARE	HIS F:147 , ASP F:149 , HIS F:162 , HIS F:175	BINDING SITE FOR RESIDUE ZN F 998
8	AC8	SOFTWARE	HIS F:197 , HIS F:201 , HIS F:207 , HOH Y:59 , HOH Y:401	BINDING SITE FOR RESIDUE ZN F 999

(no "SS Bond" information available for 2OY2)

Asymmetric Unit

No.	Residues
1	Asn A:188	-	Tyr A:189
2	Asn F:188	-	Tyr F:189

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025038	G	154	E	MMP8_HUMAN	Polymorphism	35056226	A/F	G	134	E
2	UniProt	VAR_025039	D	193	V	MMP8_HUMAN	Polymorphism	34428739	A/F	D	173	V
3	UniProt	VAR_025040	N	246	Y	MMP8_HUMAN	Polymorphism	35243553	A/F	N	226	Y

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025038	G	154	E	MMP8_HUMAN	Polymorphism	35056226	A	G	134	E
2	UniProt	VAR_025039	D	193	V	MMP8_HUMAN	Polymorphism	34428739	A	D	173	V
3	UniProt	VAR_025040	N	246	Y	MMP8_HUMAN	Polymorphism	35243553	A	N	226	Y

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025038	G	154	E	MMP8_HUMAN	Polymorphism	35056226	F	G	134	E
2	UniProt	VAR_025039	D	193	V	MMP8_HUMAN	Polymorphism	34428739	F	D	173	V
3	UniProt	VAR_025040	N	246	Y	MMP8_HUMAN	Polymorphism	35243553	F	N	226	Y

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP8_HUMAN	214-223	2	A:194-203 F:194-203

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP8_HUMAN	214-223	1	A:194-203 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP8_HUMAN	214-223	1	- F:194-203

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000236826	2b	ENSE00002164267	chr11:102595685-102595485	201	MMP8_HUMAN	1-34	34	0	-	-
1.6c	ENST00000236826	6c	ENSE00001770190	chr11:102593404-102593160	245	MMP8_HUMAN	35-116	82	2	A:86-96 F:86-96	11 11
1.7	ENST00000236826	7	ENSE00000795297	chr11:102592493-102592345	149	MMP8_HUMAN	116-166	51	2	A:96-146 F:96-146	51 51
1.8b	ENST00000236826	8b	ENSE00000795296	chr11:102592257-102592132	126	MMP8_HUMAN	166-208	43	2	A:146-188 F:146-188	43 43
1.9	ENST00000236826	9	ENSE00001105479	chr11:102589306-102589145	162	MMP8_HUMAN	208-262	55	2	A:188-242 F:188-242	55 55
1.10	ENST00000236826	10	ENSE00001105482	chr11:102587150-102587033	118	MMP8_HUMAN	262-301	40	2	A:242-242 F:242-242	1 1
1.11	ENST00000236826	11	ENSE00001105475	chr11:102586168-102586035	134	MMP8_HUMAN	301-346	46	0	-	-
1.12	ENST00000236826	12	ENSE00001105489	chr11:102585440-102585287	154	MMP8_HUMAN	346-397	52	0	-	-
1.13	ENST00000236826	13	ENSE00001105495	chr11:102584588-102584485	104	MMP8_HUMAN	397-432	36	0	-	-
1.14c	ENST00000236826	14c	ENSE00001322445	chr11:102584188-102582526	1663	MMP8_HUMAN	432-467	36	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
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Chain A from PDB  Type:PROTEIN  Length:157
 aligned with MMP8_HUMAN | P22894 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:157
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       
           MMP8_HUMAN   106 PKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 262
               SCOP domains d2oy2a_ A: Neutrophil collagenase (MMP-8)                                                                                                                     SCOP domains
               CATH domains 2oy2A00 A:86-242 Collagenase (Catalytic Domain)                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee............hhhhhhhhhhhhhh..........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------E--------------------------------------V----------------------------------------------------Y---------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c  -------------------------------------------------Exon 1.8b  PDB: A:146-188 UniProt: 166-208 -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.7  PDB: A:96-146 UniProt: 116-166           -----------------------------------------Exon 1.9  PDB: A:188-242 UniProt: 208-262               Transcript 1 (2)
                 2oy2 A  86 PKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 242
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235

Chain F from PDB  Type:PROTEIN  Length:157
 aligned with MMP8_HUMAN | P22894 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:157
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       
           MMP8_HUMAN   106 PKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 262
               SCOP domains d2oy2f_ F: Neutrophil collagenase (MMP-8)                                                                                                                     SCOP domains
               CATH domains 2oy2F00 F:86-242 Collagenase (Catalytic Domain)                                                                                                               CATH domains
           Pfam domains (1) -Peptidase_M10-2oy2F01 F:87-242                                                                                                                               Pfam domains (1)
           Pfam domains (2) -Peptidase_M10-2oy2F02 F:87-242                                                                                                                               Pfam domains (2)
         Sec.struct. author ......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee............hhhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------E--------------------------------------V----------------------------------------------------Y---------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6c  -------------------------------------------------Exon 1.8b  PDB: F:146-188 UniProt: 166-208 -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.7  PDB: F:96-146 UniProt: 116-166           -----------------------------------------Exon 1.9  PDB: F:188-242 UniProt: 208-262               Transcript 1 (2)
                 2oy2 F  86 PKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 242
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235

Chain W from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2oy2 W 207 IAG 209

Chain Y from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2oy2 Y 207 IAG 209

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: Zincin-like (701)

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

Family: Matrix metalloproteases, catalytic domain (199)

Protein domain: Neutrophil collagenase (MMP-8) (22)

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

1a	d2oy2a_	A:
1b	d2oy2f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Collagenase (Catalytic Domain) (236)

Homologous Superfamily: Collagenase (Catalytic Domain) (234)

Human (Homo sapiens) (153)

1a	2oy2A00	A:86-242
1b	2oy2F00	F:86-242

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M10 (85)

Homo sapiens (Human) (82)

1a	Peptidase_M10-2oy2F01	F:87-242
1b	Peptidase_M10-2oy2F02	F:87-242

Asymmetric Unit(hide GO term definitions)

Chain A,F (MMP8_HUMAN | P22894)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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: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:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0035987	endodermal cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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.

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		Asn A:188 - Tyr A:189	[ RasMol ]
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	2oy2
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1bzs	CRYSTAL STRUCTURE OF MMP8 COMPLEXED WITH HMR2909
2oxu
2oxw
2oxz
2oy4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

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Exons (5, 10)

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