1SU3 - 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 :   X-RAY STRUCTURE OF HUMAN PROMMP-1: NEW INSIGHTS INTO COLLAGENASE ACTION

Authors :   D. Jozic, G. Bourenkov, N. H. Lim, H. Nagase, W. Bode, K. Maskos, Structural Proteomics In Europe (Spine)

Date :   26 Mar 04 (Deposition) - 21 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: B  (8x)

Keywords :   Prodomain, Hemopexin Domain, Exocite, Structural Proteomics In Europe, Spine, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Jozic, G. Bourenkov, N. H. Lim, R. Visse, H. Nagase, W. Bode, K. Maskos
X-Ray Structure Of Human Prommp-1: New Insights Into Procollagenase Activation And Collagen Binding.
J. Biol. Chem. V. 280 9578 2005
PubMed-ID: 15611040 | Reference-DOI: 10.1074/JBC.M411084200
(for further references see the PDB file header)

Molecule 1 - INTERSTITIAL COLLAGENASE
	Chains	:	A, B
	EC Number	:	3.4.24.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MMP1, CLG
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MATRIX METALLOPROTEINASE-1, MMP-1, FIBROBLAST COLLAGENASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (8x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 22)

No.	Name	Count	Type	Full Name
1	CA	8	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	NA	2	Ligand/Ion	SODIUM ION
5	SO4	5	Ligand/Ion	SULFATE ION
6	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	CL	-1	Ligand/Ion	CHLORIDE ION
3	EPE	-1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	1	Ligand/Ion	SULFATE ION
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	4	Ligand/Ion	SULFATE ION
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 40)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EPE	8	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	32	Ligand/Ion	SULFATE ION
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:157 , ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:1027	BINDING SITE FOR RESIDUE CA A 901
02	AC2	SOFTWARE	ASP A:124 , GLU A:199 , GLU A:201 , HOH A:946 , HOH A:991	BINDING SITE FOR RESIDUE CA A 902
03	AC3	SOFTWARE	ASP A:175 , GLY A:176 , GLY A:178 , ASN A:180 , ASP A:198 , GLU A:201	BINDING SITE FOR RESIDUE CA A 903
04	AC4	SOFTWARE	ASP A:285 , GLU A:329 , ASP A:378 , ASP A:427 , HOH A:916 , HOH A:961 , HOH A:1052	BINDING SITE FOR RESIDUE CA A 904
05	AC5	SOFTWARE	ALA B:157 , ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194	BINDING SITE FOR RESIDUE CA B 905
06	AC6	SOFTWARE	ASP B:175 , GLY B:176 , GLY B:178 , ASN B:180 , ASP B:198 , GLU B:201	BINDING SITE FOR RESIDUE CA B 906
07	AC7	SOFTWARE	ASP B:124 , GLU B:199 , GLU B:201 , HOH B:1085	BINDING SITE FOR RESIDUE CA B 907
08	AC8	SOFTWARE	ASP B:285 , GLU B:329 , ASP B:378 , ASP B:427 , HOH B:1052 , HOH B:1053 , HOH B:1080	BINDING SITE FOR RESIDUE CA B 908
09	AC9	SOFTWARE	ILE A:287 , ALA A:331 , ALA A:380 , VAL A:429 , NA A:911	BINDING SITE FOR RESIDUE CL A 909
10	BC1	SOFTWARE	ILE B:287 , ALA B:331 , ALA B:380 , ALA B:428 , VAL B:429 , NA B:912	BINDING SITE FOR RESIDUE CL B 910
11	BC2	SOFTWARE	ILE A:287 , ALA A:331 , ALA A:380 , VAL A:429 , CL A:909 , HOH A:1088	BINDING SITE FOR RESIDUE NA A 911
12	BC3	SOFTWARE	ILE B:287 , ALA B:331 , ALA B:380 , VAL B:429 , CL B:910 , HOH B:980	BINDING SITE FOR RESIDUE NA B 912
13	BC4	SOFTWARE	CYS A:92 , HIS A:218 , HIS A:222 , HIS A:228	BINDING SITE FOR RESIDUE ZN A 913
14	BC5	SOFTWARE	HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196	BINDING SITE FOR RESIDUE ZN A 915
15	BC6	SOFTWARE	CYS B:92 , HIS B:218 , HIS B:222 , HIS B:228	BINDING SITE FOR RESIDUE ZN B 913
16	BC7	SOFTWARE	HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196	BINDING SITE FOR RESIDUE ZN B 915
17	BC8	SOFTWARE	PRO B:189 , GLY B:190 , LYS B:404	BINDING SITE FOR RESIDUE SO4 B 500
18	BC9	SOFTWARE	ASP B:167 , HIS B:168 , ARG B:169 , ASP B:170 , ASN B:171 , PRO B:173 , HOH B:946	BINDING SITE FOR RESIDUE SO4 B 501
19	CC1	SOFTWARE	PRO B:126 , ARG B:127	BINDING SITE FOR RESIDUE SO4 B 504
20	CC2	SOFTWARE	SER B:142 , THR B:145 , SER B:263 , GLN B:264 , ASN B:265 , HOH B:918	BINDING SITE FOR RESIDUE SO4 B 503
21	CC3	SOFTWARE	PRO A:126 , ARG A:127 , LYS A:404 , HOH A:1050 , HOH A:1104	BINDING SITE FOR RESIDUE SO4 A 801
22	CC4	SOFTWARE	VAL B:94 , PRO B:95 , SER B:172 , ALA B:184 , PHE B:185 , GLN B:186 , HOH B:959	BINDING SITE FOR RESIDUE EPE B 600

Asymmetric Unit

No.	Residues
1	A:278	-	A:466

Asymmetric Unit

No.	Residues
1	Glu A:209	-	Tyr A:210
2	Tyr A:360	-	Pro A:361
3	Ser B:57	-	Gly B:58
4	Glu B:209	-	Tyr B:210
5	Tyr B:360	-	Pro B:361
6	Tyr B:411	-	Pro B:412

Asymmetric Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021024	I	191	V	MMP1_HUMAN	Polymorphism	17879973	A/B	I	191	V
2	UniProt	VAR_011970	D	252	G	MMP1_HUMAN	Polymorphism	513964	A/B	D	252	G
3	UniProt	VAR_054005	R	262	S	MMP1_HUMAN	Polymorphism	12282811	A/B	R	262	S
4	UniProt	VAR_021025	R	405	Q	MMP1_HUMAN	Polymorphism	17879165	A/B	R	405	Q
5	UniProt	VAR_021026	S	406	T	MMP1_HUMAN	Polymorphism	17884120	A/B	S	406	T

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

Biological Unit 1 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021024	I	191	V	MMP1_HUMAN	Polymorphism	17879973	A	I	191	V
2	UniProt	VAR_011970	D	252	G	MMP1_HUMAN	Polymorphism	513964	A	D	252	G
3	UniProt	VAR_054005	R	262	S	MMP1_HUMAN	Polymorphism	12282811	A	R	262	S
4	UniProt	VAR_021025	R	405	Q	MMP1_HUMAN	Polymorphism	17879165	A	R	405	Q
5	UniProt	VAR_021026	S	406	T	MMP1_HUMAN	Polymorphism	17884120	A	S	406	T

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

Biological Unit 2 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021024	I	191	V	MMP1_HUMAN	Polymorphism	17879973	B	I	191	V
2	UniProt	VAR_011970	D	252	G	MMP1_HUMAN	Polymorphism	513964	B	D	252	G
3	UniProt	VAR_054005	R	262	S	MMP1_HUMAN	Polymorphism	12282811	B	R	262	S
4	UniProt	VAR_021025	R	405	Q	MMP1_HUMAN	Polymorphism	17879165	B	R	405	Q
5	UniProt	VAR_021026	S	406	T	MMP1_HUMAN	Polymorphism	17884120	B	S	406	T

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

Biological Unit 3 (5, 40)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021024	I	191	V	MMP1_HUMAN	Polymorphism	17879973	B	I	191	V
2	UniProt	VAR_011970	D	252	G	MMP1_HUMAN	Polymorphism	513964	B	D	252	G
3	UniProt	VAR_054005	R	262	S	MMP1_HUMAN	Polymorphism	12282811	B	R	262	S
4	UniProt	VAR_021025	R	405	Q	MMP1_HUMAN	Polymorphism	17879165	B	R	405	Q
5	UniProt	VAR_021026	S	406	T	MMP1_HUMAN	Polymorphism	17884120	B	S	406	T

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

Asymmetric Unit (4, 14)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTEINE_SWITCH	PS00546	Matrixins cysteine switch.	MMP1_HUMAN	90-97	2	A:90-97 B:90-97
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP1_HUMAN	215-224	2	A:215-224 B:215-224
3	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	MMP1_HUMAN	275-324 325-371 374-422 423-466	8	A:275-324 B:275-324 A:325-371 B:325-371 A:374-422 B:374-422 A:423-466 B:423-465
4	HEMOPEXIN	PS00024	Hemopexin domain signature.	MMP1_HUMAN	317-332	2	A:317-332 B:317-332

Biological Unit 1 (4, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTEINE_SWITCH	PS00546	Matrixins cysteine switch.	MMP1_HUMAN	90-97	1	A:90-97 -
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP1_HUMAN	215-224	1	A:215-224 -
3	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	MMP1_HUMAN	275-324 325-371 374-422 423-466	4	A:275-324 - A:325-371 - A:374-422 - A:423-466 -
4	HEMOPEXIN	PS00024	Hemopexin domain signature.	MMP1_HUMAN	317-332	1	A:317-332 -

Biological Unit 2 (4, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTEINE_SWITCH	PS00546	Matrixins cysteine switch.	MMP1_HUMAN	90-97	1	- B:90-97
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP1_HUMAN	215-224	1	- B:215-224
3	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	MMP1_HUMAN	275-324 325-371 374-422 423-466	4	- B:275-324 - B:325-371 - B:374-422 - B:423-465
4	HEMOPEXIN	PS00024	Hemopexin domain signature.	MMP1_HUMAN	317-332	1	- B:317-332

Biological Unit 3 (4, 56)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTEINE_SWITCH	PS00546	Matrixins cysteine switch.	MMP1_HUMAN	90-97	8	- B:90-97
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP1_HUMAN	215-224	8	- B:215-224
3	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	MMP1_HUMAN	275-324 325-371 374-422 423-466	32	- B:275-324 - B:325-371 - B:374-422 - B:423-465
4	HEMOPEXIN	PS00024	Hemopexin domain signature.	MMP1_HUMAN	317-332	8	- B:317-332

Asymmetric Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000315274	1	ENSE00001234609	chr11:102668891-102668719	173	MMP1_HUMAN	1-35	35	2	A:32-35 B:31-35	4 5
1.2	ENST00000315274	2	ENSE00000993211	chr11:102668231-102667987	245	MMP1_HUMAN	36-117	82	2	A:36-117 (gaps) B:36-117 (gaps)	82 82
1.3	ENST00000315274	3	ENSE00000993213	chr11:102667893-102667745	149	MMP1_HUMAN	117-167	51	2	A:117-167 B:117-167	51 51
1.4	ENST00000315274	4	ENSE00001105440	chr11:102667520-102667395	126	MMP1_HUMAN	167-209	43	2	A:167-209 B:167-209	43 43
1.5	ENST00000315274	5	ENSE00000993197	chr11:102666338-102666183	156	MMP1_HUMAN	209-261	53	2	A:209-261 B:209-261	53 53
1.6	ENST00000315274	6	ENSE00000993183	chr11:102666022-102665905	118	MMP1_HUMAN	261-300	40	2	A:261-300 B:261-300	40 40
1.7	ENST00000315274	7	ENSE00000993195	chr11:102663469-102663336	134	MMP1_HUMAN	300-345	46	2	A:300-345 B:300-345	46 46
1.8	ENST00000315274	8	ENSE00000993199	chr11:102662226-102662064	163	MMP1_HUMAN	345-399	55	2	A:345-399 B:345-399	55 55
1.9	ENST00000315274	9	ENSE00000993204	chr11:102661537-102661434	104	MMP1_HUMAN	399-434	36	2	A:399-434 B:399-434	36 36
1.10	ENST00000315274	10	ENSE00001234621	chr11:102661252-102660651	602	MMP1_HUMAN	434-469	36	2	A:434-466 B:434-465	33 32

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:415
 aligned with MMP1_HUMAN | P03956 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:435
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461     
           MMP1_HUMAN    32 DLVQKYLEKYYNLKNDGRQVEKRRNSGPVVEKLKQMQEFFGLKVTGKPDAETLKVMKQPRCGVPDVAQFVLTEGNPRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRSQNPVQPIGPQTPKACDSKLTFDAITTIRGEVMFFKDRFYMRTNPFYPEVELNFISVFWPQLPNGLEAAYEFADRDEVRFFKGNKYWAVQGQNVLHGYPKDIYSSFGFPRTVKHIDAALSEENTGKTYFFVANKYWRYDEYKRSMDPGYPKMIAHDFPGIGHKVDAVFMKDGFFYFFHGTRQYKFDPKTKRILTLQKANSWFNC 466
               SCOP domains d1su3a1 A:32-9            8 Fibroblast collagenase (MMP-1)                 d1su3a3 A:107-270 Fibroblast collagenase (MMP-1)                                                                                                                    d1su3a2 A:271-465 Collagenase (MMP1), C-terminal domain                                                                                                                                            - SCOP domains
               CATH domains 1su3A01 A:32-2            69 Collagenase (Catalytic Domain)                                                                                                                                                                                   1su3A02 A:270-466 Hemopexin                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...------------hhhhhhhhhhhhhh........hhhhhhhhh..........--------......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee............hhhhhhhhhhhhhh........................hhhhhhhhhhhhh........................eeeee..eeeeee..eeee........eeee.hhh.........eeeeehhhheeeeee..eeeeee..ee.....eehhhhhh.........eeee.....eeeeee..eeeeee....ee.....eehhhhh........eeeee..eeeeee..eeeeee....eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------G---------S----------------------------------------------------------------------------------------------------------------------------------------------QT------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------CYSTEINE---------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------------------HEMOPEXIN_2  PDB: A:275-324 UniProt: 275-324      HEMOPEXIN_2  PDB: A:325-371 UniProt: 325-371   --HEMOPEXIN_2  PDB: A:374-422 UniProt: 374-422     HEMOPEXIN_2  PDB: A:423-466 UniProt: 423-466 PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOPEXIN       -------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1 Exon 1.2  PDB: A:36-117 (gaps) UniProt: 36-117                                    -------------------------------------------------Exon 1.4  PDB: A:167-209 UniProt: 167-209  ---------------------------------------------------Exon 1.6  PDB: A:261-300                --------------------------------------------Exon 1.8  PDB: A:345-399 UniProt: 345-399              ----------------------------------Exon 1.10  PDB: A:434-466         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.3  PDB: A:117-167 UniProt: 117-167          -----------------------------------------Exon 1.5  PDB: A:209-261 UniProt: 209-261            --------------------------------------Exon 1.7  PDB: A:300-345 UniProt: 300-345     -----------------------------------------------------Exon 1.9  PDB: A:399-434            -------------------------------- Transcript 1 (2)
                 1su3 A  32 DLVQKYLEKYYNLK------------GPVVEKLKQMQEFFGLKVTGKPDAETLKVMKQPRCGVPDVA--------PRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRSQNPVQPIGPQTPKACDSKLTFDAITTIRGEVMFFKDRFYMRTNPFYPEVELNFISVFWPQLPNGLEAAYEFADRDEVRFFKGNKYWAVQGQNVLHGYPKDIYSSFGFPRTVKHIDAALSEENTGKTYFFVANKYWRYDEYKRSMDPGYPKMIAHDFPGIGHKVDAVFMKDGFFYFFHGTRQYKFDPKTKRILTLQKANSWFNC 466
                                    41   |     -      | 61        71        81        91      |  -     | 111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461     
                                        45           58                                      98      107

Chain B from PDB  Type:PROTEIN  Length:416
 aligned with MMP1_HUMAN | P03956 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:435
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460     
           MMP1_HUMAN    31 VDLVQKYLEKYYNLKNDGRQVEKRRNSGPVVEKLKQMQEFFGLKVTGKPDAETLKVMKQPRCGVPDVAQFVLTEGNPRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRSQNPVQPIGPQTPKACDSKLTFDAITTIRGEVMFFKDRFYMRTNPFYPEVELNFISVFWPQLPNGLEAAYEFADRDEVRFFKGNKYWAVQGQNVLHGYPKDIYSSFGFPRTVKHIDAALSEENTGKTYFFVANKYWRYDEYKRSMDPGYPKMIAHDFPGIGHKVDAVFMKDGFFYFFHGTRQYKFDPKTKRILTLQKANSWFN 465
               SCOP domains -d1su3b1 B:32-9           8 Fibroblast collagenase (MMP-1)                  d1su3b3 B:107-270 Fibroblast collagenase (MMP-1)                                                                                                                    d1su3b2 B:271-465 Collagenase (MMP1), C-terminal domain                                                                                                                                             SCOP domains
               CATH domains 1su3B01 B:31-26           9 Collagenase (Catalytic Domain)                                                                                                                                                                                     1su3B02 B:270-465 Hemopexin                                                                                                                                                                          CATH domains
           Pfam domains (1) PG_binding_1-1s           u3B01 B:31-87                  -----------        -Peptidase_M10-1su3B03 B:108-261                                                                                                                           --------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1su3B05 B:426-465              Pfam domains (1)
           Pfam domains (2) PG_binding_1-1s           u3B02 B:31-87                  -----------        -Peptidase_M10-1su3B04 B:108-261                                                                                                                           --------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1su3B06 B:426-465              Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1su3B07 B:426-465              Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1su3B08 B:426-465              Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1su3B09 B:426-465              Pfam domains (5)
           Pfam domains (6) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1su3B10 B:426-465              Pfam domains (6)
           Pfam domains (7) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1su3B11 B:426-465              Pfam domains (7)
           Pfam domains (8) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Hemopexin-1su3B12 B:426-465              Pfam domains (8)
         Sec.struct. author hhhhhhhhhhhh...-----------.hhhhhhhhhhhhhh........hhhhhhhhhh.........--------......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee............hhhhhhhhhhhhhhh.......................hhhhhhhhhhhhh........................eeeee..eeeeee..eeee........eeee.hhh.........eeeeehhhheeeeee..eeeeee..ee.....eehhhhhh.........eeee.....eeeeee..eeeeee....ee.....eehhhhh........eeeee..eeeeee..eeeeee....eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------G---------S----------------------------------------------------------------------------------------------------------------------------------------------QT----------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------CYSTEINE---------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------------------HEMOPEXIN_2  PDB: B:275-324 UniProt: 275-324      HEMOPEXIN_2  PDB: B:325-371 UniProt: 325-371   --HEMOPEXIN_2  PDB: B:374-422 UniProt: 374-422     HEMOPEXIN_2  PDB: B:423-465                 PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOPEXIN       ------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1  Exon 1.2  PDB: B:36-117 (gaps) UniProt: 36-117                                    -------------------------------------------------Exon 1.4  PDB: B:167-209 UniProt: 167-209  ---------------------------------------------------Exon 1.6  PDB: B:261-300                --------------------------------------------Exon 1.8  PDB: B:345-399 UniProt: 345-399              ----------------------------------Exon 1.10  PDB: B:434-465        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------Exon 1.3  PDB: B:117-167 UniProt: 117-167          -----------------------------------------Exon 1.5  PDB: B:209-261 UniProt: 209-261            --------------------------------------Exon 1.7  PDB: B:300-345 UniProt: 300-345     -----------------------------------------------------Exon 1.9  PDB: B:399-434            ------------------------------- Transcript 1 (2)
                 1su3 B  31 VDLVQKYLEKYYNLK-----------SGPVVEKLKQMQEFFGLKVTGKPDAETLKVMKQPRCGVPDVA--------PRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRSQNPVQPIGPQTPKACDSKLTFDAITTIRGEVMFFKDRFYMRTNPFYPEVELNFISVFWPQLPNGLEAAYEFADRDEVRFFKGNKYWAVQGQNVLHGYPKDIYSSFGFPRTVKHIDAALSEENTGKTYFFVANKYWRYDEYKRSMDPGYPKMIAHDFPGIGHKVDAVFMKDGFFYFFHGTRQYKFDPKTKRILTLQKANSWFN 465
                                    40    |    -      | 60        70        80        90       | -      |110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460     
                                         45          57                                       98      107

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

)

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	1su3A01	A:32-269
1b	1su3B01	B:31-269

Class: Mainly Beta (13760)

Architecture: 4 Propellor (14)

Topology: Hemopexin (14)

Homologous Superfamily: Hemopexin (14)

Human (Homo sapiens) (10)

2a	1su3A02	A:270-466
2b	1su3B02	B:270-465

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PGBD (5)

Family: PG_binding_1 (4)

Homo sapiens (Human) (3)

1a	PG_binding_1-1su3B01	B:31-87
1b	PG_binding_1-1su3B02	B:31-87

Clan: Peptidase_MA (251)

Family: Peptidase_M10 (85)

Homo sapiens (Human) (82)

2a	Peptidase_M10-1su3B03	B:108-261
2b	Peptidase_M10-1su3B04	B:108-261

Clan: no clan defined [family: Hemopexin] (5)

Family: Hemopexin (5)

Homo sapiens (Human) (3)

3a	Hemopexin-1su3B05	B:426-465
3b	Hemopexin-1su3B06	B:426-465
3c	Hemopexin-1su3B07	B:426-465
3d	Hemopexin-1su3B08	B:426-465
3e	Hemopexin-1su3B09	B:426-465
3f	Hemopexin-1su3B10	B:426-465
3g	Hemopexin-1su3B11	B:426-465
3h	Hemopexin-1su3B12	B:426-465

Asymmetric Unit(hide GO term definitions)

Chain A,B (MMP1_HUMAN | P03956)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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: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: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:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0032461	positive regulation of protein oligomerization	Any process that activates or increases the frequency, rate or extent of protein oligomerization.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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: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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	1su3
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	MMP1_HUMAN \| P03956	:	1ayk 1cge 1cgf 1cgl 1hfc 2ayk 2clt 2j0t 2tcl 3ayk 3shi 4auo 4ayk 966c

(no "Related Entries Specified in the PDB File" available for 1SU3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 22)

Sites (22, 22)

SS Bonds (1, 1)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 10)

PROSITE Motifs (4, 14)

Exons (10, 20)

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