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(-) Description

Title :  S100A12 COMPLEX WITH ZINC IN THE ABSENCE OF CALCIUM
 
Authors :  O. V. Moroz, E. V. Blagova, A. J. Wilkinson, K. S. Wilson, I. B. Bronstei
Date :  10 Mar 09  (Deposition) - 23 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Calcium Signalling, Ef-Hand, Calcium Free, S100 Protein, Host-Parasite Response, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. V. Moroz, E. V. Blagova, A. J. Wilkinson, K. S. Wilson, I. B. Bronstei
The Crystal Structures Of Human S100A12 In Apo Form And In Complex With Zinc: New Insights Into S100A12 Oligomerisation.
J. Mol. Biol. V. 391 536 2009
PubMed-ID: 19501594  |  Reference-DOI: 10.1016/J.JMB.2009.06.004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN S100-A12
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE60
    Expression System Taxid562
    FragmentRESIDUES 2-92
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymS100 CALCIUM-BINDING PROTEIN A12, CALGRANULIN-C, CGRP, NEUTROPHIL S100 PROTEIN, CALCIUM-BINDING PROTEIN IN AMNIOTIC FLUID1, P6, CAGC, CAAF1S100A12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x)AB  
Biological Unit 3 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2NA4Ligand/IonSODIUM ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2NA-1Ligand/IonSODIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CIT-1Ligand/IonCITRIC ACID
2NA-1Ligand/IonSODIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2NA-1Ligand/IonSODIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:18 , LYS A:21 , HIS A:23 , THR A:26 , HOH A:2042 , HOH A:2063BINDING SITE FOR RESIDUE NA A 92
2AC2SOFTWAREHIS A:15 , ASP A:25 , HIS B:85 , HIS B:89BINDING SITE FOR RESIDUE ZN A 95
3AC3SOFTWARESER C:18 , LYS C:21 , HIS C:23 , THR C:26 , HOH C:2051 , HOH C:2092BINDING SITE FOR RESIDUE NA B 92
4AC4SOFTWAREHIS A:85 , HIS A:89 , HIS B:15 , ASP B:25BINDING SITE FOR RESIDUE ZN B 95
5AC5SOFTWARESER B:18 , LYS B:21 , HIS B:23 , THR B:26 , HOH B:2055 , HOH B:2108BINDING SITE FOR RESIDUE NA C 92
6AC6SOFTWAREHIS C:15 , ASP C:25 , HIS D:85 , HIS D:89BINDING SITE FOR RESIDUE ZN C 95
7AC7SOFTWAREILE C:74 , SER C:75 , HOH C:2115 , HOH C:2116 , HOH C:2117 , HOH C:2118 , HOH C:2119 , LYS D:50 , SER D:75BINDING SITE FOR RESIDUE CIT C1092
8AC8SOFTWARESER D:18 , LYS D:21 , HIS D:23 , THR D:26 , HOH D:2057 , HOH D:2110BINDING SITE FOR RESIDUE NA D 92
9AC9SOFTWAREHIS C:85 , HIS C:89 , HIS D:15 , ASP D:25BINDING SITE FOR RESIDUE ZN D 95

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WC8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WC8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WC8)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10AC_HUMAN49-84
 
 
 
  4A:48-83
B:48-83
C:48-83
D:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10AC_HUMAN57-78
 
 
 
  4A:56-77
B:56-77
C:56-77
D:56-77
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10AC_HUMAN49-84
 
 
 
  4A:48-83
B:48-83
C:48-83
D:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10AC_HUMAN57-78
 
 
 
  4A:56-77
B:56-77
C:56-77
D:56-77
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10AC_HUMAN49-84
 
 
 
  2A:48-83
B:48-83
-
-
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10AC_HUMAN57-78
 
 
 
  2A:56-77
B:56-77
-
-
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10AC_HUMAN49-84
 
 
 
  2-
-
C:48-83
D:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10AC_HUMAN57-78
 
 
 
  2-
-
C:56-77
D:56-77

(-) Exons   (2, 8)

Asymmetric Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003687371aENSE00001935189chr1:153348125-15334802898S10AC_HUMAN-00--
1.2ENST000003687372ENSE00001072568chr1:153347088-153346931158S10AC_HUMAN1-46464A:0-45
B:0-45
C:0-45
D:0-45
46
46
46
46
1.4aENST000003687374aENSE00001447874chr1:153346443-153346184260S10AC_HUMAN47-92464A:46-91 (gaps)
B:46-91
C:46-91 (gaps)
D:46-91
46
46
46
46

(-) 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:88
 aligned with S10AC_HUMAN | P80511 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
           S10AC_HUMAN    1 MTKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYHTHKE 92
               SCOP domains d2wc8a_ A: automated matches                                                                 SCOP domains
               CATH domains 2wc8A00 A:0-91 EF-hand                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....----.eehhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: A:48-83             -------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: A:56-7-------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: A:0-45 UniProt: 1-46           Exon 1.4a  PDB: A:46-91 (gaps) UniProt: 47-92  Transcript 1
                  2wc8 A  0 STKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDA----QVDFQEFISLVAIALKAAHYHTHKE 91
                                     9        19        29        39        49        59  |    |69        79        89  
                                                                                         62   67                        

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with S10AC_HUMAN | P80511 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
           S10AC_HUMAN    1 MTKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYHTHKE 92
               SCOP domains d2wc8b_ B: automated matches                                                                 SCOP domains
               CATH domains 2wc8B00 B:0-91 EF-hand                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhh.....hhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: B:48-83             -------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: B:56-7-------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: B:0-45 UniProt: 1-46           Exon 1.4a  PDB: B:46-91 UniProt: 47-92         Transcript 1
                  2wc8 B  0 STKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYHTHKE 91
                                     9        19        29        39        49        59        69        79        89  

Chain C from PDB  Type:PROTEIN  Length:91
 aligned with S10AC_HUMAN | P80511 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
           S10AC_HUMAN    1 MTKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYHTHKE 92
               SCOP domains d2wc8c_ C: automated matches                                                                 SCOP domains
               CATH domains 2wc8C00 C:0-91 EF-hand                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..-.....eehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: C:48-83             -------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: C:56-7-------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: C:0-45 UniProt: 1-46           Exon 1.4a  PDB: C:46-91 (gaps) UniProt: 47-92  Transcript 1
                  2wc8 C  0 STKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGL-ANQDEQVDFQEFISLVAIALKAAHYHTHKE 91
                                     9        19        29        39        49        59| |     69        79        89  
                                                                                       60 |                             
                                                                                         62                             

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with S10AC_HUMAN | P80511 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:93
                             1                                                                                           
                             |       9        19        29        39        49        59        69        79        89   
           S10AC_HUMAN    - -MTKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYHTHKE 92
               SCOP domains d2wc8d_ D: automated matches                                                                  SCOP domains
               CATH domains 2wc8D00 D:-1-91 EF-hand                                                                       CATH domains
           Pfam domains (1) ----S_100-2wc8D01 D:3-46                        --------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----S_100-2wc8D02 D:3-46                        --------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----S_100-2wc8D03 D:3-46                        --------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----S_100-2wc8D04 D:3-46                        --------------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhhhhhh.hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------EF_HAND_2  PDB: D:48-83             -------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------S100_CABP  PDB: D:56-7-------------- PROSITE (2)
               Transcript 1 -Exon 1.2  PDB: D:0-45 UniProt: 1-46           Exon 1.4a  PDB: D:46-91 UniProt: 47-92         Transcript 1
                  2wc8 D -1 GSTKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYHTHKE 91
                                     8        18        28        38        48        58        68        78        88   

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (S10AC_HUMAN | P80511)
molecular function
    GO:0050786    RAGE receptor binding    Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0050663    cytokine secretion    The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    GO:0045576    mast cell activation    The change in morphology and behavior of a mast cell resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the mast cell has specifically bound via IgE bound to Fc-epsilonRI receptors.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        S10AC_HUMAN | P805111e8a 1gqm 1odb 2m9g 2wcb 2wce 2wcf

(-) Related Entries Specified in the PDB File

1e8a THE THREE-DIMENSIONAL STRUCTURE OF HUMAN S100A12
1gqm THE STRUCTURE OF S100A12 IN A HEXAMERIC FORM AND ITS PROPOSED ROLE IN RECEPTOR SIGNALLING
1odb THE CRYSTAL STRUCTURE OF HUMAN S100A12 - COPPER COMPLEX
2wcb S100A12 COMPLEX WITH ZINC IN THE ABSENCE OF CALCIUM
2wce CALCIUM-FREE S100A12
2wcf CALCIUM-FREE S100A12