1MMP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   MATRILYSIN COMPLEXED WITH CARBOXYLATE INHIBITOR

Authors :   M. F. Browner, W. W. Smith, A. L. Castelhano

Date :   22 Mar 95 (Deposition) - 03 Apr 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. F. Browner, W. W. Smith, A. L. Castelhano
Matrilysin-Inhibitor Complexes: Common Themes Among Metalloproteases.
Biochemistry V. 34 6602 1995
PubMed-ID: 7756291 | Reference-DOI: 10.1021/BI00020A004
(for further references see the PDB file header)

Molecule 1 - GELATINASE A
	Chains	:	A, B
	EC Number	:	3.4.24.23
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Organ	:	OVARY
	Organism Common	:	HUMAN
	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	CA	4	Ligand/Ion	CALCIUM ION
2	RSS	2	Ligand/Ion	5-METHYL-3-(9-OXO-1,8-DIAZA-TRICYCLO[10.6.1.013,18]NONADECA-12(19),13,15,17-TETRAEN-10-YLCARBAMOYL)-HEXANOIC ACID
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	RSS	1	Ligand/Ion	5-METHYL-3-(9-OXO-1,8-DIAZA-TRICYCLO[10.6.1.013,18]NONADECA-12(19),13,15,17-TETRAEN-10-YLCARBAMOYL)-HEXANOIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	RSS	1	Ligand/Ion	5-METHYL-3-(9-OXO-1,8-DIAZA-TRICYCLO[10.6.1.013,18]NONADECA-12(19),13,15,17-TETRAEN-10-YLCARBAMOYL)-HEXANOIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:218 , HIS A:222 , HIS A:228 , RSS A:269	BINDING SITE FOR RESIDUE ZN A 1
02	AC2	SOFTWARE	HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196	BINDING SITE FOR RESIDUE ZN A 2
03	AC3	SOFTWARE	ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:313 , HOH A:369	BINDING SITE FOR RESIDUE CA A 3
04	AC4	SOFTWARE	ASP A:175 , GLY A:176 , GLY A:178 , THR A:180 , ASP A:198 , GLU A:201	BINDING SITE FOR RESIDUE CA A 4
05	AC5	SOFTWARE	HIS B:218 , HIS B:222 , HIS B:228 , RSS B:269	BINDING SITE FOR RESIDUE ZN B 1
06	AC6	SOFTWARE	HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196	BINDING SITE FOR RESIDUE ZN B 2
07	AC7	SOFTWARE	ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:341	BINDING SITE FOR RESIDUE CA B 3
08	AC8	SOFTWARE	ASP B:175 , GLY B:176 , GLY B:178 , THR B:180 , ASP B:198 , GLU B:201	BINDING SITE FOR RESIDUE CA B 4
09	AC9	SOFTWARE	ZN A:1 , ASN A:179 , LEU A:181 , ALA A:182 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , PRO A:238 , THR A:239 , TYR A:240 , HOH A:318 , PRO B:232 , ASN B:242	BINDING SITE FOR RESIDUE RSS A 269
10	BC1	SOFTWARE	PRO A:232 , ASN A:242 , ZN B:1 , ASN B:179 , LEU B:181 , ALA B:182 , HIS B:218 , GLU B:219 , HIS B:222 , HIS B:228 , PRO B:238 , THR B:239 , TYR B:240 , HOH B:352 , HOH B:353 , HOH B:355	BINDING SITE FOR RESIDUE RSS B 269

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

(no "Cis Peptide Bond" information available for 1MMP)

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021027	G	137	D	MMP7_HUMAN	Polymorphism	17884789	A/B	G	142	D
2	UniProt	VAR_021028	P	241	L	MMP7_HUMAN	Polymorphism	17886506	A/B	P	245	L

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021027	G	137	D	MMP7_HUMAN	Polymorphism	17884789	A	G	142	D
2	UniProt	VAR_021028	P	241	L	MMP7_HUMAN	Polymorphism	17886506	A	P	245	L

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021027	G	137	D	MMP7_HUMAN	Polymorphism	17884789	B	G	142	D
2	UniProt	VAR_021028	P	241	L	MMP7_HUMAN	Polymorphism	17886506	B	P	245	L

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.	MMP7_HUMAN	211-220	2	A:215-224 B:215-224

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.	MMP7_HUMAN	211-220	1	A:215-224 -

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.	MMP7_HUMAN	211-220	1	- B:215-224

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000260227	1a	ENSE00002145134	chr11:102401484-102401324	161	MMP7_HUMAN	1-36	36	0	-	-
1.2	ENST00000260227	2	ENSE00000930299	chr11:102398714-102398488	227	MMP7_HUMAN	37-112	76	2	A:100-117 B:100-117	18 18
1.3a	ENST00000260227	3a	ENSE00000930298	chr11:102398403-102398255	149	MMP7_HUMAN	112-162	51	2	A:117-167 B:117-167	51 51
1.4a	ENST00000260227	4a	ENSE00000930297	chr11:102395795-102395667	129	MMP7_HUMAN	162-205	44	2	A:167-209 B:167-209	44 44
1.5	ENST00000260227	5	ENSE00000930296	chr11:102394132-102393971	162	MMP7_HUMAN	205-259	55	2	A:209-263 B:209-263	55 55
1.6	ENST00000260227	6	ENSE00001252223	chr11:102391535-102391239	297	MMP7_HUMAN	259-267	9	2	A:263-264 B:263-264	2 2

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:166
 aligned with MMP7_HUMAN | P09237 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:166
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
          MMP7_HUMAN     95 YSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGK  260
               SCOP domains d1mmpa_ A: Matrilysin (MMP-7)                                                                                                                                          SCOP domains
               CATH domains 1mmpA00 A:100-264 Collagenase (Catalytic Domain)                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh......eeeeee........hhhhhhhhhhhhhhhhhh...eeee.......eeeeee.................eee..........eeee..............hhhhhhhhhhhhh...........................hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------D-------------------------------------------------------------------------------------------------------L------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4a  PDB: A:167-209 UniProt: 162-205  -----------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3a  PDB: A:117-167 UniProt: 112-162         ------------------------------------------Exon 1.5  PDB: A:209-263 UniProt: 205-259              - Transcript 1 (2)
                1mmp A  100 YSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGK  264
                                   109       119       129       139       149       159       169       179       189       199      208B       218       228       238       248       258      
                                                                                                                                      208B

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with MMP7_HUMAN | P09237 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:166
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
          MMP7_HUMAN     95 YSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGK  260
               SCOP domains d1mmpb_ B: Matrilysin (MMP-7)                                                                                                                                          SCOP domains
               CATH domains 1mmpB00 B:100-264 Collagenase (Catalytic Domain)                                                                                                                       CATH domains
           Pfam domains (1) --------Peptidase_M10-1mmpB01 B:108-263                                                                                                                              - Pfam domains (1)
           Pfam domains (2) --------Peptidase_M10-1mmpB02 B:108-263                                                                                                                              - Pfam domains (2)
         Sec.struct. author ....hhh......eeeeee........hhhhhhhhhhhhhhhhhh...eeee.......eeeeee.................eee..........eeee..............hhhhhhhhhhhhh...........................hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------D-------------------------------------------------------------------------------------------------------L------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4a  PDB: B:167-209 UniProt: 162-205  -----------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3a  PDB: B:117-167 UniProt: 112-162         ------------------------------------------Exon 1.5  PDB: B:209-263 UniProt: 205-259              - Transcript 1 (2)
                1mmp B  100 YSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGK  264
                                   109       119       129       139       149       159       169       179       189       199      208B       218       228       238       248       258      
                                                                                                                                      208B

Legend:		→ Mismatch	(orange background)
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	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: Matrilysin (MMP-7) (3)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d1mmpa_	A:
1b	d1mmpb_	B:

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	1mmpA00	A:100-264
1b	1mmpB00	B:100-264

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M10 (85)

Homo sapiens (Human) (82)

1a	Peptidase_M10-1mmpB01	B:108-263
1b	Peptidase_M10-1mmpB02	B:108-263

Asymmetric Unit(hide GO term definitions)

Chain A,B (MMP7_HUMAN | P09237)

molecular function
	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: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:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0071260	cellular response to mechanical stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	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:0044849	estrous cycle	A type of ovulation cycle, which occurs in most mammalian therian females, where the endometrium is resorbed if pregnancy does not occur.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0060135	maternal process involved in female pregnancy	A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0031667	response to nutrient levels	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 reflecting the presence, absence, or concentration of nutrients.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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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	MMP7_HUMAN \| P09237	:	1mmq 1mmr 2ddy 2mze 2mzh 2mzi 2y6c 2y6d

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