3LJZ - 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)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN MMP-13 COMPLEXED WITH AN AMINO-2-INDANOL COMPOUND

Authors :   H. -S. Shieh, J. R. Kiefer

Date :   26 Jan 10 (Deposition) - 02 Feb 11 (Release) - 06 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Mmp-13 Inhibitor; Zinc Chelating Agent; S1' Pocket, Collagen Degradation, Disease Mutation, Disulfide Bond, Extracellular Matrix, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted, Zymogen, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. S. Shieh, A. G. Tomasselli, K. J. Mathis, M. E. Schnute, S. S. Woodard N. Caspers, J. M. Williams, J. R. Kiefer, G. Munie, A. Wittwer, A. M. Malfait, M. D. Tortorella
Structure Analysis Reveals The Flexibility Of The Adamts-5 Active Site.
Protein Sci. V. 20 735 2011
PubMed-ID: 21370305 | Reference-DOI: 10.1002/PRO.606

Molecule 1 - COLLAGENASE 3
	Chains	:	A, B, C, D
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEMEX1
	Expression System Strain	:	BL21(DE3)/PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 104-267
	Gene	:	MMP13
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MATRIX METALLOPROTEINASE-13, MMP-13

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 33)

No.	Name	Count	Type	Full Name
1	CA	8	Ligand/Ion	CALCIUM ION
2	EPE	4	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	LA3	4	Ligand/Ion	(2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BENZYL]-N~4~-HYDROXY-N~1~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]BUTANEDIAMIDE
4	SO4	9	Ligand/Ion	SULFATE ION
5	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	LA3	1	Ligand/Ion	(2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BENZYL]-N~4~-HYDROXY-N~1~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]BUTANEDIAMIDE
4	SO4	2	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	LA3	1	Ligand/Ion	(2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BENZYL]-N~4~-HYDROXY-N~1~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]BUTANEDIAMIDE
4	SO4	2	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	LA3	1	Ligand/Ion	(2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BENZYL]-N~4~-HYDROXY-N~1~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]BUTANEDIAMIDE
4	SO4	2	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (3, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	LA3	1	Ligand/Ion	(2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BENZYL]-N~4~-HYDROXY-N~1~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]BUTANEDIAMIDE
4	SO4	3	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (33, 33)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:161 , ASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:280 , HOH A:340	BINDING SITE FOR RESIDUE CA A 996
02	AC2	SOFTWARE	ASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205	BINDING SITE FOR RESIDUE CA A 997
03	AC3	SOFTWARE	HIS A:172 , ASP A:174 , HIS A:187 , HIS A:200	BINDING SITE FOR RESIDUE ZN A 998
04	AC4	SOFTWARE	HIS A:222 , HIS A:226 , HIS A:232 , LA3 A:801	BINDING SITE FOR RESIDUE ZN A 999
05	AC5	SOFTWARE	HOH A:43 , TYR A:120 , LYS A:139 , ARG A:155	BINDING SITE FOR RESIDUE SO4 A 1
06	AC6	SOFTWARE	LYS A:115 , MET A:116 , ASN A:117	BINDING SITE FOR RESIDUE SO4 A 5
07	AC7	SOFTWARE	LEU A:184 , LEU A:185 , ALA A:186 , LEU A:218 , HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , HOH A:291 , HOH A:292 , ZN A:999	BINDING SITE FOR RESIDUE LA3 A 801
08	AC8	SOFTWARE	ALA B:161 , ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198	BINDING SITE FOR RESIDUE CA B 996
09	AC9	SOFTWARE	ASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205	BINDING SITE FOR RESIDUE CA B 997
10	BC1	SOFTWARE	HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200	BINDING SITE FOR RESIDUE ZN B 998
11	BC2	SOFTWARE	HIS B:222 , HIS B:226 , HIS B:232 , LA3 B:802	BINDING SITE FOR RESIDUE ZN B 999
12	BC3	SOFTWARE	HOH B:4 , HOH B:87 , TYR B:176 , PRO B:190 , ASP B:231 , HIS B:232 , HOH B:277	BINDING SITE FOR RESIDUE EPE B 3
13	BC4	SOFTWARE	HOH B:77 , HOH B:92 , LYS B:139 , ARG B:155 , HOH B:298	BINDING SITE FOR RESIDUE SO4 B 2
14	BC5	SOFTWARE	PRO A:236 , LYS B:115 , MET B:116 , ASN B:117 , HOH B:307 , HOH B:312	BINDING SITE FOR RESIDUE SO4 B 6
15	BC6	SOFTWARE	HOH A:98 , HOH B:4 , GLY B:183 , LEU B:184 , LEU B:185 , ALA B:186 , LEU B:218 , HIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , ALA B:238 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , ZN B:999	BINDING SITE FOR RESIDUE LA3 B 802
16	BC7	SOFTWARE	ALA C:161 , ASP C:162 , ASN C:194 , GLY C:196 , ASP C:198	BINDING SITE FOR RESIDUE CA C 996
17	BC8	SOFTWARE	ASP C:179 , GLY C:180 , SER C:182 , LEU C:184 , ASP C:202 , GLU C:205	BINDING SITE FOR RESIDUE CA C 997
18	BC9	SOFTWARE	HIS C:172 , ASP C:174 , HIS C:187 , HIS C:200	BINDING SITE FOR RESIDUE ZN C 998
19	CC1	SOFTWARE	HIS C:222 , HIS C:226 , HIS C:232 , LA3 C:803	BINDING SITE FOR RESIDUE ZN C 999
20	CC2	SOFTWARE	TYR C:176 , LEU C:184 , HIS C:187 , ALA C:188 , PHE C:189 , PRO C:190	BINDING SITE FOR RESIDUE EPE C 1
21	CC3	SOFTWARE	HOH C:45 , TYR C:120 , LYS C:139 , ARG C:155 , HOH C:311	BINDING SITE FOR RESIDUE SO4 C 3
22	CC4	SOFTWARE	LYS C:115 , MET C:116 , ASN C:117	BINDING SITE FOR RESIDUE SO4 C 7
23	CC5	SOFTWARE	HOH C:10 , LEU C:184 , LEU C:185 , ALA C:186 , LEU C:218 , HIS C:222 , GLU C:223 , HIS C:226 , HIS C:232 , ALA C:238 , LEU C:239 , PHE C:241 , PRO C:242 , ILE C:243 , TYR C:244 , THR C:245 , ZN C:999	BINDING SITE FOR RESIDUE LA3 C 803
24	CC6	SOFTWARE	HOH D:57 , ASP D:162 , ASN D:194 , GLY D:196 , ASP D:198	BINDING SITE FOR RESIDUE CA D 996
25	CC7	SOFTWARE	ASP D:179 , GLY D:180 , SER D:182 , LEU D:184 , ASP D:202 , GLU D:205	BINDING SITE FOR RESIDUE CA D 997
26	CC8	SOFTWARE	HIS D:172 , ASP D:174 , HIS D:187 , HIS D:200	BINDING SITE FOR RESIDUE ZN D 998
27	CC9	SOFTWARE	HIS D:222 , HIS D:226 , HIS D:232 , LA3 D:804	BINDING SITE FOR RESIDUE ZN D 999
28	DC1	SOFTWARE	PRO B:193 , ASN B:194 , TYR D:176 , LEU D:184 , HIS D:187 , PHE D:189 , PRO D:190 , HOH D:289	BINDING SITE FOR RESIDUE EPE D 2
29	DC2	SOFTWARE	GLU D:133 , ALA D:137 , LYS D:140 , SER D:209 , PHE D:217 , HOH D:271 , HOH D:350	BINDING SITE FOR RESIDUE EPE D 4
30	DC3	SOFTWARE	HOH D:7 , LYS D:139 , ARG D:155 , HOH D:321	BINDING SITE FOR RESIDUE SO4 D 268
31	DC4	SOFTWARE	LYS D:115 , MET D:116 , ASN D:117	BINDING SITE FOR RESIDUE SO4 D 8
32	DC5	SOFTWARE	PRO D:108 , ARG D:109	BINDING SITE FOR RESIDUE SO4 D 9
33	DC6	SOFTWARE	HOH D:26 , GLY D:183 , LEU D:184 , LEU D:185 , ALA D:186 , LEU D:218 , HIS D:222 , GLU D:223 , HIS D:226 , HIS D:232 , ALA D:238 , LEU D:239 , PHE D:241 , PRO D:242 , ILE D:243 , TYR D:244 , THR D:245 , HOH D:307 , HOH D:312 , ZN D:999	BINDING SITE FOR RESIDUE LA3 D 804

(no "SS Bond" information available for 3LJZ)

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

Asymmetric Unit (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073418	W	207	G	MMP13_HUMAN	Disease (MDST)	140059558	A/B/C/D	W	207	G
2	UniProt	VAR_063434	H	232	N	MMP13_HUMAN	Disease (MANDP1)	121909500	A/B/C/D	H	232	N

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_073418	W	207	G	MMP13_HUMAN	Disease (MDST)	140059558	A	W	207	G
2	UniProt	VAR_063434	H	232	N	MMP13_HUMAN	Disease (MANDP1)	121909500	A	H	232	N

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_073418	W	207	G	MMP13_HUMAN	Disease (MDST)	140059558	B	W	207	G
2	UniProt	VAR_063434	H	232	N	MMP13_HUMAN	Disease (MANDP1)	121909500	B	H	232	N

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

Biological Unit 3 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073418	W	207	G	MMP13_HUMAN	Disease (MDST)	140059558	C	W	207	G
2	UniProt	VAR_063434	H	232	N	MMP13_HUMAN	Disease (MANDP1)	121909500	C	H	232	N

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

Biological Unit 4 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073418	W	207	G	MMP13_HUMAN	Disease (MDST)	140059558	D	W	207	G
2	UniProt	VAR_063434	H	232	N	MMP13_HUMAN	Disease (MANDP1)	121909500	D	H	232	N

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP13_HUMAN	219-228	4	A:219-228 B:219-228 C:219-228 D:219-228

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.	MMP13_HUMAN	219-228	1	A:219-228 - - -

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.	MMP13_HUMAN	219-228	1	- B:219-228 - -

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.	MMP13_HUMAN	219-228	1	- - C:219-228 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP13_HUMAN	219-228	1	- - - D:219-228

Asymmetric Unit (5, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000260302	1a	ENSE00001105391	chr11:102826463-102826315	149	MMP13_HUMAN	1-40	40	0	-	-
1.2	ENST00000260302	2	ENSE00001105386	chr11:102826222-102825981	242	MMP13_HUMAN	41-121	81	4	A:104-121 B:104-121 C:104-121 D:104-121	18 18 18 18
1.3	ENST00000260302	3	ENSE00001105401	chr11:102825335-102825187	149	MMP13_HUMAN	121-171	51	4	A:121-171 B:121-171 C:121-171 D:121-171	51 51 51 51
1.4	ENST00000260302	4	ENSE00001105398	chr11:102825010-102824885	126	MMP13_HUMAN	171-213	43	4	A:171-213 B:171-213 C:171-213 D:171-213	43 43 43 43
1.5	ENST00000260302	5	ENSE00001139473	chr11:102822902-102822741	162	MMP13_HUMAN	213-267	55	4	A:213-267 (gaps) B:213-267 C:213-267 D:213-267	55 55 55 55
1.6	ENST00000260302	6	ENSE00000930343	chr11:102820956-102820839	118	MMP13_HUMAN	267-306	40	4	A:267-267 B:267-267 C:267-267 D:267-267	1 1 1 1
1.7	ENST00000260302	7	ENSE00000930342	chr11:102819887-102819754	134	MMP13_HUMAN	306-351	46	0	-	-
1.8	ENST00000260302	8	ENSE00000930341	chr11:102818779-102818620	160	MMP13_HUMAN	351-404	54	0	-	-
1.9	ENST00000260302	9	ENSE00000930340	chr11:102816478-102816375	104	MMP13_HUMAN	404-439	36	0	-	-
1.11b	ENST00000260302	11b	ENSE00002188786	chr11:102815095-102813724	1372	MMP13_HUMAN	439-471	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:161
 aligned with MMP13_HUMAN | P45452 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:164
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
          MMP13_HUMAN   104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG 267
               SCOP domains d3ljza_ A: Collagenase-3 (MMP-13)                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh..................---....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------G------------------------N----------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4  PDB: A:171-213 UniProt: 171-213  -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: A:121-171 UniProt: 121-171          -----------------------------------------Exon 1.5  PDB: A:213-267 (gaps) UniProt: 213-267        Transcript 1 (2)
                 3ljz A 104 ANVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYT---HFMLPDDDVQGIQSLYG 267
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243   |   253       263    
                                                                                                                                                                         247 251

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with MMP13_HUMAN | P45452 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:164
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
          MMP13_HUMAN   104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG 267
               SCOP domains d3ljzb_ B: Collagenase-3 (MMP-13)                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------G------------------------N----------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4  PDB: B:171-213 UniProt: 171-213  -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: B:121-171 UniProt: 121-171          -----------------------------------------Exon 1.5  PDB: B:213-267 UniProt: 213-267               Transcript 1 (2)
                 3ljz B 104 ANVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG 267
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

Chain C from PDB  Type:PROTEIN  Length:164
 aligned with MMP13_HUMAN | P45452 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:164
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
          MMP13_HUMAN   104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG 267
               SCOP domains d3ljzc_ C: Collagenase-3 (MMP-13)                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------G------------------------N----------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4  PDB: C:171-213 UniProt: 171-213  -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: C:121-171 UniProt: 121-171          -----------------------------------------Exon 1.5  PDB: C:213-267 UniProt: 213-267               Transcript 1 (2)
                 3ljz C 104 ANVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG 267
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

Chain D from PDB  Type:PROTEIN  Length:164
 aligned with MMP13_HUMAN | P45452 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:164
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
          MMP13_HUMAN   104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG 267
               SCOP domains d3ljzd_ D: Collagenase-3 (MMP-13)                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------Peptidase_M10-3ljzD01 D:112-267                                                                                                                              Pfam domains (1)
           Pfam domains (2) --------Peptidase_M10-3ljzD02 D:112-267                                                                                                                              Pfam domains (2)
           Pfam domains (3) --------Peptidase_M10-3ljzD03 D:112-267                                                                                                                              Pfam domains (3)
           Pfam domains (4) --------Peptidase_M10-3ljzD04 D:112-267                                                                                                                              Pfam domains (4)
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------G------------------------N----------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4  PDB: D:171-213 UniProt: 171-213  -----------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: D:121-171 UniProt: 121-171          -----------------------------------------Exon 1.5  PDB: D:213-267 UniProt: 213-267               Transcript 1 (2)
                 3ljz D 104 ANVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYG 267
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

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: Collagenase-3 (MMP-13) (31)

Human (Homo sapiens) [TaxId: 9606] (30)

1a	d3ljza_	A:
1b	d3ljzb_	B:
1c	d3ljzc_	C:
1d	d3ljzd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M10 (85)

Homo sapiens (Human) (82)

1a	Peptidase_M10-3ljzD01	D:112-267
1b	Peptidase_M10-3ljzD02	D:112-267
1c	Peptidase_M10-3ljzD03	D:112-267
1d	Peptidase_M10-3ljzD04	D:112-267

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MMP13_HUMAN | P45452)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	GO:0001968	fibronectin binding	Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
	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:0050750	low-density lipoprotein particle receptor binding	Interacting selectively and non-covalently with a low-density lipoprotein receptor.
	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:0030282	bone mineralization	The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue.
	GO:0060349	bone morphogenesis	The process in which bones are generated and organized.
	GO:0051216	cartilage development	The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0071498	cellular response to fluid shear stress	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 fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
	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:0035116	embryonic hindlimb morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
	GO:0001958	endochondral ossification	Replacement ossification wherein bone tissue replaces cartilage.
	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:0003417	growth plate cartilage development	The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0001554	luteolysis	The lysis or structural demise of the corpus luteum. During normal luteolysis, two closely related events occur. First, there is loss of the capacity to synthesize and secrete progesterone (functional luteolysis) followed by loss of the cells that comprise the corpus luteum (structural luteolysis). Preventing luteolysis is crucial to maintain pregnancy.
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0001649	osteoblast differentiation	The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
	GO:0007567	parturition	The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs.
	GO:0043171	peptide catabolic process	The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
	GO:1904244	positive regulation of pancreatic trypsinogen secretion	Any process that activates or increases the frequency, rate or extent of pancreatic trypsinogen secretion.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0043627	response to estrogen	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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
	GO:0001666	response to hypoxia	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 indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0009612	response to mechanical stimulus	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 mechanical stimulus.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	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:0046581	intercellular canaliculus	An extremely narrow tubular channel located between adjacent cells. An instance of this is the secretory canaliculi occurring between adjacent parietal cells in the gastric mucosa of vertebrates.
	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.
	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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EPE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		LA3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]
		CC9	[ RasMol ]	+environment [ RasMol ]
		DC1	[ RasMol ]	+environment [ RasMol ]
		DC2	[ RasMol ]	+environment [ RasMol ]
		DC3	[ RasMol ]	+environment [ RasMol ]
		DC4	[ RasMol ]	+environment [ RasMol ]
		DC5	[ RasMol ]	+environment [ RasMol ]
		DC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ljz)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3ljz
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	MMP13_HUMAN \| P45452
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.24.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	250400
		Disease Information	:	OMIM
	602111
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	MMP13_HUMAN \| P45452
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

3hy9	THE SAME PROTEIN COMPLEXED WITH INHIBITOR OF SAME CHEMICAL CLASS
3hyg	THE SAME PROTEIN COMPLEXED WITH INHIBITOR OF SAME CHEMICAL CLASS
3ljt	SAME INHIBITOR IN THE CATALYTIC DOMAIN OF ADAMTS-5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 33)

Sites (33, 33)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 8)

PROSITE Motifs (1, 4)

Exons (5, 20)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (42, 42)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File