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(-) Description

Title :  MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8 FROM HUMAN
 
Authors :  K. Ishikawa, A. Nakagawa, I. Tanaka, J. Nishihira
Date :  13 Apr 99  (Deposition) - 17 May 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Calcium-Binding Protein, Mad, Migration Inhibitory Factor_ Related Protein 8, S100 Protein, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Ishikawa, A. Nakagawa, I. Tanaka, M. Suzuki, J. Nishihira
The Structure Of Human Mrp8, A Member Of The S100 Calcium-Binding Protein Family, By Mad Phasing At 1. 9 A Resolution.
Acta Crystallogr. , Sect. D V. 56 559 2000
PubMed-ID: 10771424  |  Reference-DOI: 10.1107/S0907444900002833

(-) Compounds

Molecule 1 - MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
    CellLYMPHOCYTE
    ChainsA, B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMRP8, S100A8, CALGRANULIN A
    TissueBLOOD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:59 , ASN A:61 , ASP A:63 , ALA A:65 , GLU A:70 , HOH A:140BINDING SITE FOR RESIDUE CA A 101
2AC2SOFTWARESER A:20 , LYS A:23 , ASN A:25 , ALA A:28 , TYR A:30 , HOH A:141BINDING SITE FOR RESIDUE CA A 102
3AC3SOFTWAREASP B:59 , ASN B:61 , ASP B:63 , ALA B:65 , GLU B:70 , HOH B:165BINDING SITE FOR RESIDUE CA B 101
4AC4SOFTWARESER B:20 , LYS B:23 , ASN B:25 , ALA B:28 , HOH B:166BINDING SITE FOR RESIDUE CA B 102
5EF1AUTHORSER A:20 , LYS A:23 , ASN A:25 , ALA A:28CALCIUM BINDING SITE IN EF HAND
6EF2AUTHORASP A:59 , ASN A:61 , ASP A:63 , ALA A:65CALCIUM BINDING SITE IN EF HAND
7EF3AUTHORSER B:20 , LYS B:23 , ASN B:25 , ALA B:28CALCIUM BINDING SITE IN EF HAND
8EF4AUTHORASP B:59 , ASN B:61 , ASP B:63 , ALA B:65CALCIUM BINDING SITE IN EF HAND

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MR8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MR8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MR8)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10A8_HUMAN46-81
 
  2A:46-81
B:46-81
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10A8_HUMAN54-75
 
  2A:54-75
B:54-75
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S10A8_HUMAN59-71
 
  2A:59-71
B:59-71
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10A8_HUMAN46-81
 
  2A:46-81
B:46-81
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10A8_HUMAN54-75
 
  2A:54-75
B:54-75
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S10A8_HUMAN59-71
 
  2A:59-71
B:59-71
Biological Unit 2 (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10A8_HUMAN46-81
 
  4A:46-81
B:46-81
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10A8_HUMAN54-75
 
  4A:54-75
B:54-75
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S10A8_HUMAN59-71
 
  4A:59-71
B:59-71

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003687331aENSE00001447868chr1:153363664-153363517148S10A8_HUMAN-00--
1.1dENST000003687331dENSE00001447867chr1:153363033-153362871163S10A8_HUMAN1-47472A:1-47
B:1-47
47
47
1.2bENST000003687332bENSE00001447864chr1:153362719-153362508212S10A8_HUMAN48-93462A:48-90
B:48-90
43
43

(-) 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:90
 aligned with S10A8_HUMAN | P05109 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:90
                                    10        20        30        40        50        60        70        80        90
           S10A8_HUMAN    1 MLTELEKALNSIIDVYHKYSLIKGNFHAVYRDDLKKLLETECPQYIRKKGADVWFKELDINTDGAVNFQEFLILVIKMGVAAHKKSHEES 90
               SCOP domains d1mr8a_ A: Calcyclin (S100)                                                                SCOP domains
               CATH domains 1mr8A00 A:1-90 EF-hand                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........eehhhhhhhhhhh..hhhhhh.hhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------EF_HAND_2  PDB: A:46-81             --------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------S100_CABP  PDB: A:54-7--------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------EF_HAND_1    ------------------- PROSITE (3)
               Transcript 1 Exon 1.1d  PDB: A:1-47 UniProt: 1-47           Exon 1.2b  PDB: A:48-90 UniProt: 48-93      Transcript 1
                  1mr8 A  1 MLTELEKALNSIIDVYHKYSLIKGNFHAVYRDDLKKLLETECPQYIRKKGADVWFKELDINTDGAVNFQEFLILVIKMGVAAHKKSHEES 90
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with S10A8_HUMAN | P05109 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:90
                                    10        20        30        40        50        60        70        80        90
           S10A8_HUMAN    1 MLTELEKALNSIIDVYHKYSLIKGNFHAVYRDDLKKLLETECPQYIRKKGADVWFKELDINTDGAVNFQEFLILVIKMGVAAHKKSHEES 90
               SCOP domains d1mr8b_ B: Calcyclin (S100)                                                                SCOP domains
               CATH domains 1mr8B00 B:1-90 EF-hand                                                                     CATH domains
           Pfam domains (1) ----S_100-1mr8B01 B:5-48                        ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----S_100-1mr8B02 B:5-48                        ------------------------------------------ Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........eehhhhhhhhhhh..hhhhhh.hhhhhhhh......ee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------EF_HAND_2  PDB: B:46-81             --------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------S100_CABP  PDB: B:54-7--------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------EF_HAND_1    ------------------- PROSITE (3)
               Transcript 1 Exon 1.1d  PDB: B:1-47 UniProt: 1-47           Exon 1.2b  PDB: B:48-90 UniProt: 48-93      Transcript 1
                  1mr8 B  1 MLTELEKALNSIIDVYHKYSLIKGNFHAVYRDDLKKLLETECPQYIRKKGADVWFKELDINTDGAVNFQEFLILVIKMGVAAHKKSHEES 90
                                    10        20        30        40        50        60        70        80        90

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (47, 47)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (S10A8_HUMAN | P05109)
molecular function
    GO:0050786    RAGE receptor binding    Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
    GO:0035662    Toll-like receptor 4 binding    Interacting selectively and non-covalently with a Toll-like 4 protein, a pattern recognition receptor that binds bacterial lipopolysaccharide (LPS) to initiate an innate immune response.
    GO:0050544    arachidonic acid binding    Interacting selectively and non-covalently with arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0002526    acute inflammatory response    Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0014002    astrocyte development    The process aimed at the progression of an astrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0032602    chemokine production    The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0002544    chronic inflammatory response    Inflammation of prolonged duration (weeks or months) in which active inflammation, tissue destruction, and attempts at repair are proceeding simultaneously. Although it may follow acute inflammation, chronic inflammation frequently begins insidiously, as a low-grade, smoldering, often asymptomatic response.
    GO:0001816    cytokine production    The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    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:0002523    leukocyte migration involved in inflammatory response    The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response.
    GO:0070488    neutrophil aggregation    The adhesion of one neutrophil to one or more other neutrophils via adhesion molecules.
    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:0018119    peptidyl-cysteine S-nitrosylation    The covalent addition of a nitric oxide (NO) group to the sulphur (S) atom of a cysteine residue in a protein, to form peptidyl-S-nitrosyl-L-cysteine.
    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:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:2001244    positive regulation of intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:0002793    positive regulation of peptide secretion    Any process that activates or increases the frequency, rate, or extent of peptide secretion.
    GO:0051493    regulation of cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0045471    response to ethanol    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 ethanol stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0010043    response to zinc ion    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 zinc ion stimulus.
    GO:0032119    sequestering of zinc ion    The process of binding or confining zinc ions such that they are separated from other components of a biological system.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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: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)

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        S10A8_HUMAN | P051091xk4 4ggf 4xjk 5hlo 5hlv 5w1f

(-) Related Entries Specified in the PDB File

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