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(-) Description

Title :  FUNCTIONALLY SELECTIVE INHIBITION OF GROUP IIA PHOSPHOLIPASE A2 REVEALS A ROLE FOR VIMENTIN IN REGULATING ARACHIDONIC ACID METABOLISM
 
Authors :  L. K. Lee, K. J. Bryant, R. Bouveret, P. -W. Lei, A. P. Duff, S. J. Harrop, E R. P. Harvey, M. H. Gelb, P. P. Gray, P. M. Curmi, A. M. Cunningham, W. B. C K. F. Scott
Date :  17 Oct 11  (Deposition) - 17 Oct 12  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Secreted Phospholipase A2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. K. Lee, K. J. Bryant, R. Bouveret, P. W. Lei, A. P. Duff, S. J. Harrop, E. P. Huang, R. P. Harvey, M. H. Gelb, P. P. Gray, P. M. Curmi, A. M. Cunningham, W. B. Church, K. F. Scott
Selective Inhibition Of Human Group Iia-Secreted Phospholipase A2 (Hgiia) Signaling Reveals Arachidonic Acid Metabolism Is Associated With Colocalization Of Hgiia To Vimentin In Rheumatoid Synoviocytes.
J. Biol. Chem. V. 288 15269 2013
PubMed-ID: 23482564  |  Reference-DOI: 10.1074/JBC.M112.397893

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
    ChainsA, B
    EC Number3.1.1.4
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Taxid10029
    GenePLA2G2A, PLA2B, PLA2L, RASF-A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGIIC SPLA2, GROUP IIA PHOSPHOLIPASE A2, NON-PANCREATIC SECRETORY PHOSPHOLIPASE A2, NPS-PLA2, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE 2A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3NA4Ligand/IonSODIUM ION
4OLD2Mod. Amino Acid3-[2-(4-BROMOPHENYL)-2-OXOETHYL]-L-HISTIDINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
4OLD1Mod. Amino Acid3-[2-(4-BROMOPHENYL)-2-OXOETHYL]-L-HISTIDINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION
4OLD1Mod. Amino Acid3-[2-(4-BROMOPHENYL)-2-OXOETHYL]-L-HISTIDINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:23 , GLY A:25 , TYR A:112 , ASN A:114 , HOH A:401 , HOH A:403BINDING SITE FOR RESIDUE CA A 201
02AC2SOFTWAREHIS A:27 , GLY A:29 , GLY A:31 , ASP A:48 , HOH A:425 , HOH A:443BINDING SITE FOR RESIDUE CA A 202
03AC3SOFTWAREASN A:4 , ARG A:7 , ARG B:118BINDING SITE FOR RESIDUE CL A 203
04AC4SOFTWAREHOH A:294BINDING SITE FOR RESIDUE NA A 204
05AC5SOFTWARESER A:65BINDING SITE FOR RESIDUE NA A 125
06AC6SOFTWARELYS A:108 , SER B:65 , ARG B:84BINDING SITE FOR RESIDUE CL A 126
07AC7SOFTWAREPHE B:23 , GLY B:25 , TYR B:112 , ASN B:114 , HOH B:402 , HOH B:404BINDING SITE FOR RESIDUE CA B 201
08AC8SOFTWAREHIS B:27 , GLY B:29 , GLY B:31 , ASP B:48 , HOH B:428 , HOH B:442BINDING SITE FOR RESIDUE CA B 202
09AC9SOFTWAREARG A:118 , ASN B:4 , ARG B:7BINDING SITE FOR RESIDUE CL B 203
10BC1SOFTWARESER A:65 , ARG A:84 , HOH A:344 , LYS B:108BINDING SITE FOR RESIDUE CL B 125
11BC2SOFTWARESER B:65BINDING SITE FOR RESIDUE NA B 126

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:26 -A:117
2A:28 -A:44
3A:43 -A:97
4A:49 -A:124
5A:50 -A:90
6A:59 -A:83
7A:77 -A:88
8B:26 -B:117
9B:28 -B:44
10B:43 -B:97
11B:49 -B:124
12B:50 -B:90
13B:59 -B:83
14B:77 -B:88

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U8I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U8I)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2GA_HUMAN63-70
 
  2A:43-50
B:43-50
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2GA_HUMAN107-117
 
  2A:87-97
B:87-97
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2GA_HUMAN63-70
 
  1A:43-50
-
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2GA_HUMAN107-117
 
  1A:87-97
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2GA_HUMAN63-70
 
  1-
B:43-50
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2GA_HUMAN107-117
 
  1-
B:87-97

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENST000004005202cENSE00001543334chr1:20306111-2030607339PA2GA_HUMAN-00--
1.3cENST000004005203cENSE00002182826chr1:20305372-20305227146PA2GA_HUMAN1-14140--
1.3eENST000004005203eENSE00001326822chr1:20305017-20304873145PA2GA_HUMAN14-62492A:1-42
B:1-42
42
42
1.3gENST000004005203gENSE00000873019chr1:20304614-20304508107PA2GA_HUMAN62-98372A:42-78
B:42-78
37
37
1.4dENST000004005204dENSE00001543318chr1:20302336-20301929408PA2GA_HUMAN98-144472A:78-124
B:78-124
47
47

(-) 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:124
 aligned with PA2GA_HUMAN | P14555 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:124
                                    30        40        50        60        70        80        90       100       110       120       130       140    
          PA2GA_HUMAN    21 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 144
               SCOP domains d3u8ia_ A: Phospholipase A2                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ------------------------------------PA2_ASP    --------------------------- PROSITE
           Transcript 1 (1) Exon 1.3e  PDB: A:1-42 UniProt: 14-62     -----------------------------------Exon 1.4d  PDB: A:78-124 UniProt: 98-144        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3g  PDB: A:42-78              ---------------------------------------------- Transcript 1 (2)
                 3u8i A   1 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVThDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 124
                                    10        20        30        40      | 50        60        70        80        90       100       110       120    
                                                                         47-OLD                                                                         

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with PA2GA_HUMAN | P14555 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:124
                                    30        40        50        60        70        80        90       100       110       120       130       140    
          PA2GA_HUMAN    21 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 144
               SCOP domains d3u8ib_ B: Phospholipase A2                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ------------------------------------PA2_ASP    --------------------------- PROSITE
           Transcript 1 (1) Exon 1.3e  PDB: B:1-42 UniProt: 14-62     -----------------------------------Exon 1.4d  PDB: B:78-124 UniProt: 98-144        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3g  PDB: B:42-78              ---------------------------------------------- Transcript 1 (2)
                 3u8i B   1 NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVThDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 124
                                    10        20        30        40      | 50        60        70        80        90       100       110       120    
                                                                         47-OLD                                                                         

   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  (0, 0)

(no "CATH Domain" information available for 3U8I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U8I)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PA2GA_HUMAN | P14555)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0047498    calcium-dependent phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate. This reaction requires 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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
biological process
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0034374    low-density lipoprotein particle remodeling    The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
    GO:0006654    phosphatidic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
    GO:0046473    phosphatidic acid metabolic process    The chemical reactions and pathways involving phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
    GO:0036151    phosphatidylcholine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylcholine, through sequential deacylation and re-acylation reactions, to generate phosphatidylcholine containing different types of fatty acid acyl chains.
    GO:0036152    phosphatidylethanolamine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylethanolamine, through sequential deacylation and re-acylation reactions, to generate phosphatidylethanolamine containing different types of fatty acid acyl chains.
    GO:0036148    phosphatidylglycerol acyl-chain remodeling    Remodeling the acyl chains of phosphatidylglycerol, through sequential deacylation and re-acylation reactions, to generate phosphatidylglycerol containing different types of fatty acid acyl chains.
    GO:0036149    phosphatidylinositol acyl-chain remodeling    Remodeling the acyl chains of phosphatidylinositol, through sequential deacylation and re-acylation reactions, to generate phosphatidylinositol containing different types of fatty acid acyl chains.
    GO:0036150    phosphatidylserine acyl-chain remodeling    Remodeling the acyl chains of phosphatidylserine, through sequential deacylation and re-acylation reactions, to generate phosphatidylserine containing different types of fatty acid acyl chains.
    GO:0006644    phospholipid metabolic process    The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0010744    positive regulation of macrophage derived foam cell differentiation    Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PA2GA_HUMAN | P145551ayp 1bbc 1db4 1db5 1dcy 1j1a 1kqu 1kvo 1n28 1n29 1pod 1poe 2gny 3u8b 3u8d 3u8h 5g3n

(-) Related Entries Specified in the PDB File

3u8b 3u8d 3u8h