1Q3A - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MATRIX METALLOPROTEINASE 10

Authors :   V. Calderone, I. Bertini, M. Fragai, C. Luchinat, S. Mangani, B. Terni

Date :   29 Jul 03 (Deposition) - 06 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: B,C  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Mmp-10, Metalloproteinase, Inhibitors, Nngh, Stromelysin-2, Hydroxamic Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Bertini, V. Calderone, M. Fragai, C. Luchinat, S. Mangani, B. Terni
Crystal Structure Of The Catalytic Domain Of Human Matrix Metalloproteinase 10.
J. Mol. Biol. V. 336 707 2004
PubMed-ID: 15095982 | Reference-DOI: 10.1016/J.JMB.2003.12.033
(for further references see the PDB file header)

Molecule 1 - STROMELYSIN-2
	Chains	:	A, B, C
	EC Number	:	3.4.24.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	MMP10 OR STMY2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MATRIX METALLOPROTEINASE-10, MMP-10, TRANSIN-2, SL-2

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:		B	C
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	CA	9	Ligand/Ion	CALCIUM ION
2	NGH	3	Ligand/Ion	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYLHYDROXAMIC ACID
3	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NGH	2	Ligand/Ion	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYLHYDROXAMIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NGH	2	Ligand/Ion	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYLHYDROXAMIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NGH	1	Ligand/Ion	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYLHYDROXAMIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:217 , HIS A:221 , HIS A:227 , NGH A:480	BINDING SITE FOR RESIDUE ZN A 464
02	AC2	SOFTWARE	HIS A:167 , ASP A:169 , HIS A:182 , HIS A:195	BINDING SITE FOR RESIDUE ZN A 465
03	AC3	SOFTWARE	ASP A:174 , GLY A:175 , GLY A:177 , SER A:179 , ASP A:197 , GLU A:200	BINDING SITE FOR RESIDUE CA A 466
04	AC4	SOFTWARE	ASP A:157 , GLY A:189 , TYR A:191 , ASP A:193	BINDING SITE FOR RESIDUE CA A 467
05	AC5	SOFTWARE	ASP A:123 , ASP A:198 , GLU A:200 , HOH A:564 , HOH A:597	BINDING SITE FOR RESIDUE CA A 468
06	AC6	SOFTWARE	HIS B:217 , HIS B:221 , HIS B:227 , NGH B:479	BINDING SITE FOR RESIDUE ZN B 469
07	AC7	SOFTWARE	HIS B:167 , ASP B:169 , HIS B:182 , HIS B:195	BINDING SITE FOR RESIDUE ZN B 470
08	AC8	SOFTWARE	ASP B:174 , GLY B:175 , GLY B:177 , SER B:179 , ASP B:197 , GLU B:200	BINDING SITE FOR RESIDUE CA B 471
09	AC9	SOFTWARE	ASP B:157 , GLY B:189 , TYR B:191 , ASP B:193 , HOH B:513	BINDING SITE FOR RESIDUE CA B 472
10	BC1	SOFTWARE	ASP B:123 , ASP B:198 , GLU B:200 , HOH B:482 , HOH B:500	BINDING SITE FOR RESIDUE CA B 473
11	BC2	SOFTWARE	HIS C:217 , HIS C:221 , HIS C:227 , NGH C:481 , HOH C:491	BINDING SITE FOR RESIDUE ZN C 474
12	BC3	SOFTWARE	HIS C:167 , ASP C:169 , HIS C:182 , HIS C:195	BINDING SITE FOR RESIDUE ZN C 475
13	BC4	SOFTWARE	ASP C:174 , GLY C:175 , GLY C:177 , SER C:179 , ASP C:197 , GLU C:200	BINDING SITE FOR RESIDUE CA C 476
14	BC5	SOFTWARE	ASP C:157 , GLY C:189 , TYR C:191 , ASP C:193 , HOH C:498	BINDING SITE FOR RESIDUE CA C 477
15	BC6	SOFTWARE	ASP C:123 , ASP C:198 , GLU C:200	BINDING SITE FOR RESIDUE CA C 478
16	BC7	SOFTWARE	SER B:179 , LEU B:180 , ALA B:181 , LEU B:213 , HIS B:217 , GLU B:218 , HIS B:221 , HIS B:227 , PRO B:237 , TYR B:239 , ZN B:469 , HOH B:583 , HIS C:178	BINDING SITE FOR RESIDUE NGH B 479
17	BC8	SOFTWARE	HIS A:178 , SER A:179 , LEU A:180 , ALA A:181 , LEU A:213 , HIS A:217 , GLU A:218 , HIS A:221 , HIS A:227 , PRO A:237 , SER A:241 , ZN A:464 , HOH A:485 , HOH A:612 , HIS B:178	BINDING SITE FOR RESIDUE NGH A 480
18	BC9	SOFTWARE	ASN B:240 , PHE B:242 , HOH B:499 , HOH B:535 , HOH B:605 , SER C:179 , LEU C:180 , ALA C:181 , HIS C:217 , GLU C:218 , HIS C:221 , HIS C:227 , LEU C:234 , LEU C:238 , TYR C:239 , ZN C:474 , HOH C:491 , HOH C:504 , HOH C:517 , HOH C:520 , HOH C:544	BINDING SITE FOR RESIDUE NGH C 481

(no "SS Bond" information available for 1Q3A)

Asymmetric Unit

No.	Residues
1	Tyr A:239	-	Asn A:240

Asymmetric Unit (3, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036139	E	142	Q	MMP10_HUMAN	Unclassified	---	A/B/C	E	142	Q
2	CancerSNP	VAR_MMP10_HUMAN_CCDS8321_1_01 *	E	142	Q	MMP10_HUMAN	Disease (Breast cancer)	---	A/B/C	E	142	Q
3	UniProt	VAR_020952	F	226	L	MMP10_HUMAN	Polymorphism	17860971	A/B/C	F	226	L
	* ID not provided by source

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

Biological Unit 1 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036139	E	142	Q	MMP10_HUMAN	Unclassified	---	A/B	E	142	Q
2	CancerSNP	VAR_MMP10_HUMAN_CCDS8321_1_01 *	E	142	Q	MMP10_HUMAN	Disease (Breast cancer)	---	A/B	E	142	Q
3	UniProt	VAR_020952	F	226	L	MMP10_HUMAN	Polymorphism	17860971	A/B	F	226	L
	* ID not provided by source

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

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036139	E	142	Q	MMP10_HUMAN	Unclassified	---	B/C	E	142	Q
2	CancerSNP	VAR_MMP10_HUMAN_CCDS8321_1_01 *	E	142	Q	MMP10_HUMAN	Disease (Breast cancer)	---	B/C	E	142	Q
3	UniProt	VAR_020952	F	226	L	MMP10_HUMAN	Polymorphism	17860971	B/C	F	226	L
	* ID not provided by source

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

Biological Unit 3 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036139	E	142	Q	MMP10_HUMAN	Unclassified	---	C	E	142	Q
2	CancerSNP	VAR_MMP10_HUMAN_CCDS8321_1_01 *	E	142	Q	MMP10_HUMAN	Disease (Breast cancer)	---	C	E	142	Q
3	UniProt	VAR_020952	F	226	L	MMP10_HUMAN	Polymorphism	17860971	C	F	226	L
	* ID not provided by source

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP10_HUMAN	214-223	3	A:214-223 B:214-223 C:214-223

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP10_HUMAN	214-223	2	A:214-223 B:214-223 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP10_HUMAN	214-223	2	- B:214-223 C:214-223

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP10_HUMAN	214-223	1	- - C:214-223

Asymmetric Unit (5, 15)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000279441	1	ENSE00000993214	chr11:102651359-102651218	142	MMP10_HUMAN	1-35	35	0	-	-
1.2	ENST00000279441	2	ENSE00000993200	chr11:102650476-102650235	242	MMP10_HUMAN	36-116	81	3	A:105-116 B:104-116 C:106-116	12 13 11
1.3	ENST00000279441	3	ENSE00001758252	chr11:102650092-102649944	149	MMP10_HUMAN	116-166	51	3	A:116-166 B:116-166 C:116-166	51 51 51
1.4	ENST00000279441	4	ENSE00000993192	chr11:102649480-102649355	126	MMP10_HUMAN	166-208	43	3	A:166-208 B:166-208 C:166-208	43 43 43
1.5	ENST00000279441	5	ENSE00001706030	chr11:102647507-102647343	165	MMP10_HUMAN	208-263	56	3	A:208-263 (gaps) B:208-263 C:208-263 (gaps)	56 56 56
1.6	ENST00000279441	6	ENSE00000993219	chr11:102647155-102647011	145	MMP10_HUMAN	263-311	49	3	A:263-263 B:263-263 C:263-263	1 1 1
1.7	ENST00000279441	7	ENSE00000993209	chr11:102646052-102645919	134	MMP10_HUMAN	311-356	46	0	-	-
1.8	ENST00000279441	8	ENSE00001692235	chr11:102643737-102643578	160	MMP10_HUMAN	356-409	54	0	-	-
1.9	ENST00000279441	9	ENSE00000993181	chr11:102642846-102642743	104	MMP10_HUMAN	409-444	36	0	-	-
1.10	ENST00000279441	10	ENSE00000993208	chr11:102641624-102641245	380	MMP10_HUMAN	444-476	33	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:156
 aligned with MMP10_HUMAN | P09238 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:159
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
          MMP10_HUMAN   105 MPKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDFYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNSFTELAQFRLSQDDVNGIQSLYG 263
               SCOP domains d1q3aa_ A: Stromelysin-2 (MMP-10)                                                                                                                               SCOP domains
               CATH domains 1q3aA00 A:105-263 Collagenase (Catalytic Domain)                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.................---......hhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------Q-----------------------------------------------------------------------------------L------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------Q------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2    -------------------------------------------------Exon 1.4  PDB: A:166-208 UniProt: 166-208  ------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.3  PDB: A:116-166 UniProt: 116-166          -----------------------------------------Exon 1.5  PDB: A:208-263 (gaps) UniProt: 208-263         Transcript 1 (2)
                 1q3a A 105 MPKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDNYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNS---LAQFRLSQDDVNGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234      |  -|      254         
                                                                                                                                                                  241 245

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with MMP10_HUMAN | P09238 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:160
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
          MMP10_HUMAN   104 GMPKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDFYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNSFTELAQFRLSQDDVNGIQSLYG 263
               SCOP domains d1q3ab_ B: Stromelysin-2 (MMP-10)                                                                                                                                SCOP domains
               CATH domains 1q3aB00 B:104-263 Collagenase (Catalytic Domain)                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhhh...eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...........................hhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------Q-----------------------------------------------------------------------------------L------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------Q------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2     -------------------------------------------------Exon 1.4  PDB: B:166-208 UniProt: 166-208  ------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3  PDB: B:116-166 UniProt: 116-166          -----------------------------------------Exon 1.5  PDB: B:208-263 UniProt: 208-263                Transcript 1 (2)
                 1q3a B 104 GMPKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDNYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNSFTELAQFRLSQDDVNGIQSLYG 263
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with MMP10_HUMAN | P09238 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:158
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        
          MMP10_HUMAN   106 PKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDFYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNSFTELAQFRLSQDDVNGIQSLYG 263
               SCOP domains d1q3ac_ C: Stromelysin-2 (MMP-10)                                                                                                                              SCOP domains
               CATH domains 1q3aC00 C:106-263 Collagenase (Catalytic Domain)                                                                                                               CATH domains
           Pfam domains (1) -Peptidase_M10-1q3aC01 C:107-263                                                                                                                               Pfam domains (1)
           Pfam domains (2) -Peptidase_M10-1q3aC02 C:107-263                                                                                                                               Pfam domains (2)
           Pfam domains (3) -Peptidase_M10-1q3aC03 C:107-263                                                                                                                               Pfam domains (3)
         Sec.struct. author ......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..................---......hhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------Q-----------------------------------------------------------------------------------L------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------Q------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2   -------------------------------------------------Exon 1.4  PDB: C:166-208 UniProt: 166-208  ------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.3  PDB: C:116-166 UniProt: 116-166          -----------------------------------------Exon 1.5  PDB: C:208-263 (gaps) UniProt: 208-263         Transcript 1 (2)
                 1q3a C 106 PKWRKTHLTYRIVNYTPDLPRDAVDSAIEKALKVWEEVTPLTFSRLYEGEADIMISFAVKEHGDNYSFDGPGHSLAHAYPPGPGLYGDIHFDDDEKWTEDASGTNLFLVAAHELGHSLGLFHSANTEALMYPLYNS---LAQFRLSQDDVNGIQSLYG 263
                                   115       125       135       145       155       165       175       185       195       205       215       225       235     | 245       255        
                                                                                                                                                                 241 245

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: Stromelysin-2 (MMP-10) (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1q3aa_	A:
1b	d1q3ab_	B:
1c	d1q3ac_	C:

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	1q3aB00	B:104-263
1b	1q3aA00	A:105-263
1c	1q3aC00	C:106-263

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M10 (85)

Homo sapiens (Human) (82)

1a	Peptidase_M10-1q3aC01	C:107-263
1b	Peptidase_M10-1q3aC02	C:107-263
1c	Peptidase_M10-1q3aC03	C:107-263

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (MMP10_HUMAN | P09238)

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: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.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
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.

Asymmetric Unit
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	Cis Peptide Bonds
		Tyr A:239 - Asn A:240	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

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	1q3a
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		Orientation in Membranes	:	OPM
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		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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		Structural Neighbours	:	CE \| VAST
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	MMP10_HUMAN \| P09238
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	3.4.24.22
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	MMP10_HUMAN \| P09238
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	MMP10_HUMAN \| P09238	:	3v96 4ilw

1bqo	MATRIX METALLOPROTEINASE 3 IN COMPLEX WITH POTENT ACHIRAL INHIBITORS
1d5j	MMP3 COMPLEXED WITH A THIAZEPINE BASED INHIBITOR.
1d8f	MMP3 COMPLEXED WITH A PIPERAZINE BASED INHIBITOR
1g49	MMP3 IN COMPLEX WITH A CARBOXYLIC ACID BASED INHIBITOR
1uea	MMP-3/TIMP-1 COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 9)

PROSITE Motifs (1, 3)

Exons (5, 15)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (16, 16)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File