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(-) Description

Title :  HEMOPEXIN-LIKE DOMAIN OF MATRIX METALLOPROTEINASE 14
 
Authors :  A. Tochowicz, Y. Itoh, K. Maskos, W. Bode, P. Goettig
Date :  08 Feb 08  (Deposition) - 10 Feb 09  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Membrane Protein Interaction, Pro-Mmp-2, Timp-2, Metastasis, Cleavage On Pair Of Basic Residues, Hydrolase, Metal-Binding, Metalloprotease, Protease, Transmembrane, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Tochowicz, P. Goettig, R. Evans, R. Visse, Y. Shitomi, R. Palmisano N. Ito, K. Richter, K. Maskos, D. Franke, D. Svergun, H. Nagase, W. Bode Y. Itoh
The Dimer Interface Of The Membrane Type 1 Matrix Metalloproteinase Hemopexin Domain: Crystal Structure And Biological Functions
J. Biol. Chem. V. 286 7587 2011
PubMed-ID: 21193411  |  Reference-DOI: 10.1074/JBC.M110.178434

(-) Compounds

Molecule 1 - MATRIX METALLOPROTEINASE-14
    ChainsA
    EC Number3.4.24.80
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System StrainHEK 293 CELLS
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 316-511
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHEMOPEXIN 14 DOMAIN, MMP-14, MEMBRANE-TYPE MATRIX METALLOPROTEINASE 1, MT-MMP 1, MTMMP1, MEMBRANE-TYPE-1 MATRIX, METALLOPROTEINASE, MT1-MMP, MT1MMP, MMP- X1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A
Biological Unit 3 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:56 , ASN A:369 , THR A:370 , ASP A:416 , ARG A:464BINDING SITE FOR RESIDUE NA A 1001
2AC2SOFTWAREHOH A:19 , THR A:325 , ALA A:327 , THR A:370 , ALA A:371BINDING SITE FOR RESIDUE CL A 1002

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:319 -A:508

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:353 -Pro A:354
2Tyr A:399 -Pro A:400
3Tyr A:449 -Pro A:450
4Tyr A:497 -Pro A:498

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021035M355IMMP14_HUMANPolymorphism17880989AM355I
2UniProtVAR_031267R431HMMP14_HUMANPolymorphism3751489AR431H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021035M355IMMP14_HUMANPolymorphism17880989AM355I
2UniProtVAR_031267R431HMMP14_HUMANPolymorphism3751489AR431H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021035M355IMMP14_HUMANPolymorphism17880989AM355I
2UniProtVAR_031267R431HMMP14_HUMANPolymorphism3751489AR431H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021035M355IMMP14_HUMANPolymorphism17880989AM355I
2UniProtVAR_031267R431HMMP14_HUMANPolymorphism3751489AR431H

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

(-) PROSITE Motifs  (2, 5)

Asymmetric Unit (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOPEXIN_2PS51642 Hemopexin repeat profile.MMP14_HUMAN316-364
365-410
412-460
461-508
  4A:316-364
A:365-410
A:412-460
A:461-508
2HEMOPEXINPS00024 Hemopexin domain signature.MMP14_HUMAN357-372  1A:357-372
Biological Unit 1 (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOPEXIN_2PS51642 Hemopexin repeat profile.MMP14_HUMAN316-364
365-410
412-460
461-508
  4A:316-364
A:365-410
A:412-460
A:461-508
2HEMOPEXINPS00024 Hemopexin domain signature.MMP14_HUMAN357-372  1A:357-372
Biological Unit 2 (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOPEXIN_2PS51642 Hemopexin repeat profile.MMP14_HUMAN316-364
365-410
412-460
461-508
  8A:316-364
A:365-410
A:412-460
A:461-508
2HEMOPEXINPS00024 Hemopexin domain signature.MMP14_HUMAN357-372  2A:357-372
Biological Unit 3 (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEMOPEXIN_2PS51642 Hemopexin repeat profile.MMP14_HUMAN316-364
365-410
412-460
461-508
  8A:316-364
A:365-410
A:412-460
A:461-508
2HEMOPEXINPS00024 Hemopexin domain signature.MMP14_HUMAN357-372  2A:357-372

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003118521ENSE00001417791chr14:23305772-23306134363MMP14_HUMAN1-36360--
1.2ENST000003118522ENSE00001031343chr14:23310700-23310848149MMP14_HUMAN37-86500--
1.3ENST000003118523ENSE00001031341chr14:23311122-23311244123MMP14_HUMAN86-127420--
1.4ENST000003118524ENSE00001031346chr14:23311619-23311926308MMP14_HUMAN127-2301040--
1.5ENST000003118525ENSE00001031364chr14:23312466-23312627162MMP14_HUMAN230-284550--
1.6ENST000003118526ENSE00001198262chr14:23312919-23313079161MMP14_HUMAN284-337541A:316-33722
1.7ENST000003118527ENSE00001031362chr14:23313580-23313718139MMP14_HUMAN338-384471A:338-38447
1.8ENST000003118528ENSE00001031361chr14:23313839-23313989151MMP14_HUMAN384-434511A:384-43451
1.9ENST000003118529ENSE00001031354chr14:23314460-23314575116MMP14_HUMAN434-473401A:434-47340
1.10ENST0000031185210ENSE00001431522chr14:23314917-233169702054MMP14_HUMAN473-5821101A:473-51139

(-) Sequences/Alignments

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:196
 aligned with MMP14_HUMAN | P50281 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:196
                                   325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505      
          MMP14_HUMAN   316 PNICDGNFDTVAMLRGEMFVFKERWFWRVRNNQVMDGYPMPIGQFWRGLPASINTAYERKDGKFVFFKGDKHWVFDEASLEPGYPKHIKELGRGLPTDKIDAALFWMPNGKTYFFRGNKYYRFNEELRAVDSEYPKNIKVWEGIPESPRGSFMGSDEVFTYFYKGNKYWKFNNQKLKVEPGYPKSALRDWMGCPSG 511
               SCOP domains d3c7xa_ A: automated matches                                                                                                                                                                         SCOP domains
               CATH domains 3c7xA00 A:316-511 Hemopexin                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eeeee..eeeeee..eeeeee..ee.....eehhhhh........eeee.....eeeee..eeeeee..ee.....ee.hhh..........eeee......eeeee..eeeeee....ee.....ee.hhh........eeee.....eeeeee..eeeeee....ee.....eehhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------I---------------------------------------------------------------------------H-------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HEMOPEXIN_2  PDB: A:316-364 UniProt: 316-364     HEMOPEXIN_2  PDB: A:365-410 UniProt: 365-410  -HEMOPEXIN_2  PDB: A:412-460 UniProt: 412-460     HEMOPEXIN_2  PDB: A:461-508 UniProt: 461-508    --- PROSITE (1)
                PROSITE (2) -----------------------------------------HEMOPEXIN       ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.6 [INCOMPLETE] Exon 1.7  PDB: A:338-384 UniProt: 338-384      ----------------------------------------------------------------------------------------Exon 1.10  PDB: A:473-511 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.8  PDB: A:384-434 UniProt: 384-434          ----------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) ----------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:434-473                -------------------------------------- Transcript 1 (3)
                 3c7x A 316 PNICDGNFDTVAMLRGEMFVFKERWFWRVRNNQVMDGYPMPIGQFWRGLPASINTAYERKDGKFVFFKGDKHWVFDEASLEPGYPKHIKELGRGLPTDKIDAALFWMPNGKTYFFRGNKYYRFNEELRAVDSEYPKNIKVWEGIPESPRGSFMGSDEVFTYFYKGNKYWKFNNQKLKVEPGYPKSALRDWMGCPSG 511
                                   325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505      

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C7X)

(-) Gene Ontology  (55, 55)

Asymmetric Unit(hide GO term definitions)
Chain A   (MMP14_HUMAN | P50281)
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:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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:0016504    peptidase activator activity    Binds to and increases the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    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:0005515    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).
    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:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0043615    astrocyte cell migration    The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord.
    GO:0060348    bone development    The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
    GO:0048754    branching morphogenesis of an epithelial tube    The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0035988    chondrocyte proliferation    The multiplication or reproduction of chondrocytes by cell division, resulting in the expansion of their population. A chondrocyte is a polymorphic cell that forms cartilage.
    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:0097094    craniofacial suture morphogenesis    The process in which any suture between cranial and/or facial bones is generated and organized.
    GO:0048701    embryonic cranial skeleton morphogenesis    The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase.
    GO:0001958    endochondral ossification    Replacement ossification wherein bone tissue replaces cartilage.
    GO:0035987    endodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
    GO:0001935    endothelial cell proliferation    The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0045746    negative regulation of Notch signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway.
    GO:0051895    negative regulation of focal adhesion assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    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:0001541    ovarian follicle development    The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
    GO:0045579    positive regulation of B cell differentiation    Any process that activates or increases the frequency, rate or extent of B cell differentiation.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0010831    positive regulation of myotube differentiation    Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
    GO:0010952    positive regulation of peptidase activity    Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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:0009725    response to hormone    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 hormone stimulus.
    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.
    GO:0014070    response to organic cyclic compound    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 an organic cyclic compound stimulus.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0048771    tissue remodeling    The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.
    GO:0031638    zymogen activation    The proteolytic processing of an inactive enzyme to an active form.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0044354    macropinosome    A membrane-bounded, uncoated intracellular vesicle formed by the process of macropinocytosis.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  MMP14_HUMAN | P50281
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MMP14_HUMAN | P502811bqq 1buv 2mqs 3ma2 3x23 4p3c 4p3d 4qxu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3C7X)