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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST COLLAGENASE COMPLEXED WITH AN INHIBITOR

Authors :   F. K. Winkler, N. Borkakoti, A. D'Arcy

Date :   07 Sep 94 (Deposition) - 08 Mar 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

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

Reference :   N. Borkakoti, F. K. Winkler, D. H. Williams, A. D'Arcy, M. J. Broadhurst, P. A. Brown, W. H. Johnson, E. J. Murray
Structure Of The Catalytic Domain Of Human Fibroblast Collagenase Complexed With An Inhibitor.
Nat. Struct. Biol. V. 1 106 1994
PubMed-ID: 7656013 | Reference-DOI: 10.1038/NSB0294-106
(for further references see the PDB file header)

Molecule 1 - FIBROBLAST COLLAGENASE
	Chains	:	A
	Fragment	:	CATALYTIC DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	RO4	1	Ligand/Ion	[[1-[N-HYDROXY-ACETAMIDYL]-3-METHYL-BUTYL]-CARBONYL-LEUCINYL]-ALANINE ETHYL ESTER
3	SM	1	Ligand/Ion	SAMARIUM (III) ION
4	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:118 , HIS A:122 , HIS A:128 , RO4 A:175	BINDING SITE FOR RESIDUE ZN A 170
2	AC2	SOFTWARE	ASP A:24 , GLU A:99 , GLU A:101 , HOH A:195 , HOH A:217 , HOH A:218	BINDING SITE FOR RESIDUE SM A 171
3	AC3	SOFTWARE	HIS A:68 , ASP A:70 , HIS A:83 , HIS A:96	BINDING SITE FOR RESIDUE ZN A 172
4	AC4	SOFTWARE	ASP A:75 , GLY A:76 , GLY A:78 , ASN A:80 , ASP A:98 , GLU A:101	BINDING SITE FOR RESIDUE CA A 173
5	AC5	SOFTWARE	ASP A:58 , GLY A:90 , GLY A:92 , ASP A:94 , HOH A:201 , HOH A:240	BINDING SITE FOR RESIDUE CA A 174
6	AC6	SOFTWARE	GLY A:79 , ASN A:80 , LEU A:81 , ALA A:82 , PHE A:107 , TYR A:110 , HIS A:118 , GLU A:119 , HIS A:122 , HIS A:128 , PRO A:138 , SER A:139 , TYR A:140 , ZN A:170 , HOH A:176 , HOH A:177	BINDING SITE FOR RESIDUE RO4 A 175

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:109	-	Tyr A:110

Asymmetric/Biological Unit (3, 3)

								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	91	V
2	UniProt	VAR_011970	D	252	G	MMP1_HUMAN	Polymorphism	513964	A	D	152	G
3	UniProt	VAR_054005	R	262	S	MMP1_HUMAN	Polymorphism	12282811	A	R	162	S

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP1_HUMAN	215-224	1	A:115-124

Asymmetric/Biological Unit (5, 5)

	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	0	-	-
1.2	ENST00000315274	2	ENSE00000993211	chr11:102668231-102667987	245	MMP1_HUMAN	36-117	82	1	A:2-17	16
1.3	ENST00000315274	3	ENSE00000993213	chr11:102667893-102667745	149	MMP1_HUMAN	117-167	51	1	A:17-67	51
1.4	ENST00000315274	4	ENSE00001105440	chr11:102667520-102667395	126	MMP1_HUMAN	167-209	43	1	A:67-109	43
1.5	ENST00000315274	5	ENSE00000993197	chr11:102666338-102666183	156	MMP1_HUMAN	209-261	53	1	A:109-161	53
1.6	ENST00000315274	6	ENSE00000993183	chr11:102666022-102665905	118	MMP1_HUMAN	261-300	40	1	A:161-164	4
1.7	ENST00000315274	7	ENSE00000993195	chr11:102663469-102663336	134	MMP1_HUMAN	300-345	46	0	-	-
1.8	ENST00000315274	8	ENSE00000993199	chr11:102662226-102662064	163	MMP1_HUMAN	345-399	55	0	-	-
1.9	ENST00000315274	9	ENSE00000993204	chr11:102661537-102661434	104	MMP1_HUMAN	399-434	36	0	-	-
1.10	ENST00000315274	10	ENSE00001234621	chr11:102661252-102660651	602	MMP1_HUMAN	434-469	36	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:163
 aligned with MMP1_HUMAN | P03956 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:163
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
           MMP1_HUMAN   102 LTEGNPRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRSQ 264
               SCOP domains d2tcla_ A: Fibroblast collagenase (MMP-1)                                                                                                                           SCOP domains
               CATH domains 2tclA00 A:2-164 Collagenase (Catalytic Domain)                                                                                                                      CATH domains
               Pfam domains ------Peptidase_M10-2tclA01 A:8-161                                                                                                                             --- Pfam domains
         Sec.struct. author ...........eeeeee........hhhhhhhhhhhhhhhhhhh..eeee.......eeeeee.................eee..........eeee.............hhhhhhhhhhhh..........................hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------V------------------------------------------------------------G---------S-- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        -------------------------------------------------Exon 1.4  PDB: A:67-109 UniProt: 167-209   ---------------------------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.3  PDB: A:17-67 UniProt: 117-167            -----------------------------------------Exon 1.5  PDB: A:109-161 UniProt: 209-261            --- Transcript 1 (2)
                 2tcl A   2 LTEGNPRWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVSEGQADIMISFVRGDHRDNSPFDGPGGNLAHAFQPGPGIGGDAHFDEDERWTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTFSGDVQLAQDDIDGIQAIYGRSQ 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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/Biological 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: Fibroblast collagenase (MMP-1) (14)

Human (Homo sapiens) [TaxId: 9606] (13)

d2tcla_

Asymmetric/Biological 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)

2tclA00

A:2-164

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M10 (85)

Homo sapiens (Human) (82)

Peptidase_M10-2tclA01

A:8-161

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:109 - Tyr A:110	[ RasMol ]

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	MMP1_HUMAN \| P03956	:	1ayk 1cge 1cgf 1cgl 1hfc 1su3 2ayk 2clt 2j0t 3ayk 3shi 4auo 4ayk 966c

(no "Related Entries Specified in the PDB File" available for 2TCL)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

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Exons (5, 5)

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