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(-) Description

Title :  CRYSTAL STRUCTURE OF 1,3-GLUCURONYLTRANSFERASE I (GLCAT-I) COMPLEXED WITH GAL-GAL-XYL, UDP, AND MN2+
 
Authors :  L. C. Pedersen, K. Tsuchida, H. Kitagawa, K. Sugahara, T. A. Darden
Date :  28 Jul 00  (Deposition) - 31 Jan 01  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glucuronyltransferase, Udp, Ddd, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. C. Pedersen, K. Tsuchida, H. Kitagawa, K. Sugahara, T. A. Darden, M. Negishi
Heparan/Chondroitin Sulfate Biosynthesis. Structure And Mechanism Of Human Glucuronyltransferase I.
J. Biol. Chem. V. 275 34580 2000
PubMed-ID: 10946001  |  Reference-DOI: 10.1074/JBC.M007399200

(-) Compounds

Molecule 1 - GLUCURONYLTRANSFERASE I
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System Taxid562
    OrganLIVER
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2MN2Ligand/IonMANGANESE (II) ION
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
4UNX2Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGAL A:2 , VAL A:221 , GLU A:227 , TRP A:243 , ARG A:247 , ASP A:252 , GLU A:281BINDING SITE FOR RESIDUE GAL A 1
2AC2SOFTWAREGAL A:1 , GLY A:222 , TRP A:243 , HOH A:398 , GLN B:318BINDING SITE FOR RESIDUE GAL A 2
3AC3SOFTWAREASP A:196 , UDP A:337 , HOH A:339 , HOH A:340BINDING SITE FOR RESIDUE MN A 336
4AC4SOFTWAREASP B:196 , UDP B:337 , HOH B:339 , HOH B:340BINDING SITE FOR RESIDUE MN B 336
5AC5SOFTWAREPRO A:82 , THR A:83 , TYR A:84 , ASP A:113 , ARG A:156 , GLY A:157 , ASP A:194 , ASP A:195 , ASP A:196 , HIS A:308 , ARG A:310 , MN A:336 , UNX A:338 , HOH A:343 , HOH A:357 , HOH A:359BINDING SITE FOR RESIDUE UDP A 337
6AC6SOFTWAREASP A:252 , HIS A:308 , UDP A:337 , HOH A:341 , HOH A:343BINDING SITE FOR RESIDUE UNX A 338
7AC7SOFTWAREPRO B:82 , THR B:83 , TYR B:84 , ASP B:113 , ARG B:156 , GLY B:157 , ASP B:194 , ASP B:195 , ASP B:196 , HIS B:308 , ARG B:310 , MN B:336 , UNX B:338 , HOH B:339 , HOH B:340 , HOH B:350 , HOH B:380 , HOH B:413 , HOH B:438BINDING SITE FOR RESIDUE UDP B 337
8AC8SOFTWAREASP B:252 , HIS B:308 , UDP B:337 , HOH B:340 , HOH B:341 , HOH B:342BINDING SITE FOR RESIDUE UNX B 338

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075370P140LB3GA3_HUMANDisease (JDSCD)879255269A/BP140L
2UniProtVAR_075371G223SB3GA3_HUMANUnclassified (JDSCD)372487178A/BG223S
3UniProtVAR_066624R277QB3GA3_HUMANDisease (JDSCD)387906937A/BR277Q

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FGG)

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002654711aENSE00002142592chr11:62389647-62389338310B3GA3_HUMAN1-28280--
1.3ENST000002654713ENSE00001118980chr11:62388143-62387969175B3GA3_HUMAN28-86592A:75-86
B:75-86
12
12
1.4cENST000002654714cENSE00000991160chr11:62384819-62384459361B3GA3_HUMAN86-2061212A:86-206 (gaps)
B:86-206 (gaps)
121
121
1.5bENST000002654715bENSE00000991161chr11:62384268-62383978291B3GA3_HUMAN207-303972A:207-303
B:207-303 (gaps)
97
97
1.6dENST000002654716dENSE00001293049chr11:62383271-62382768504B3GA3_HUMAN304-335322A:304-335
B:304-335
32
32

(-) Sequences/Alignments

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
(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:250
 aligned with B3GA3_HUMAN | O94766 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:261
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
          B3GA3_HUMAN    75 PTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWEPSRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV 335
               SCOP domains d1fgga_ A: 1,3-Glucuronyltransferase I (glcAT-I)                                                                                                                                                                                                                      SCOP domains
               CATH domains 1fggA00 A:75-335 Spore Coat Polysaccharide Biosynthesis Protein Sp           sA; Chain A                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh.eeeeee....-----------.....hhhhhhhhhhhhh....eeee..........eeeee.....eehhhhhhhhh....eee..eeee..eeeeeeeee..eeeeee...........hhh.eeeehhhhhh.............hhhhhhhh...hhhhheehhhhhh...ee........hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------L----------------------------------------------------------------------------------S-----------------------------------------------------Q---------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3    ------------------------------------------------------------------------------------------------------------------------Exon 1.5b  PDB: A:207-303 UniProt: 207-303                                                       Exon 1.6d  PDB: A:304-335        Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4c  PDB: A:86-206 (gaps) UniProt: 86-206                                                                          --------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1fgg A  75 MTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTP-----------WVHPRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWEPSRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV 335
                                    84        94       104       114       124       134     |   -       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
                                                                                           140         152                                                                                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with B3GA3_HUMAN | O94766 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:261
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
          B3GA3_HUMAN    75 PTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWEPSRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV 335
               SCOP domains d1fggb_ B: 1,3-Glucuronyltransferase I (glcAT-I)                                                                                                                                                                                                                      SCOP domains
               CATH domains 1fggB00 B:75-335 Spore Coat Polysaccharide Biosynthesis Protein Sp             sA; Chain A                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh...eeeeee....-------------...hhhhhhhhhhhhh....eeee..........eeeee.....eehhhhhhhhh....eee..eeee..eeeeeeeee..eeeeee....--.....hhh.eeeehhhhhhh.........hhhhhhhhhhh...hhhhheehhhhhh...ee........hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------L----------------------------------------------------------------------------------S-----------------------------------------------------Q---------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3    ------------------------------------------------------------------------------------------------------------------------Exon 1.5b  PDB: B:207-303 (gaps) UniProt: 207-303                                                Exon 1.6d  PDB: B:304-335        Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4c  PDB: B:86-206 (gaps) UniProt: 86-206                                                                          --------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1fgg B  75 MTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTP-------------HPRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWE--RPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV 335
                                    84        94       104       114       124       134     |   -       154       164       174       184       194       204       214       224       234       244  |    254       264       274       284       294       304       314       324       334 
                                                                                           140           154                                                                                       244  |                                                                                        
                                                                                                                                                                                                      247                                                                                        

   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/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FGG)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B3GA3_HUMAN | O94766)
molecular function
    GO:0015018    galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity    Catalysis of the reaction: UDP-glucuronate + 3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein = UDP + 3-beta-D-glucuronosyl-3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein.
    GO:0015020    glucuronosyltransferase activity    Catalysis of the reaction: UDP-glucuronate + acceptor = UDP + acceptor beta-D-glucuronoside.
    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:0072542    protein phosphatase activator activity    Increases the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0030204    chondroitin sulfate metabolic process    The chemical reactions and pathways involving chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. They usually occur linked to a protein to form proteoglycans. Two subgroups exist, one in which the sulfate is on the 4-position (chondroitin sulfate A) and the second in which it is in the 6-position (chondroitin sulfate C). They often are polydisperse and often differ in the degree of sulfation from tissue to tissue. The chains of repeating disaccharide are covalently linked to the side chains of serine residues in the polypeptide backbone of a protein by a glycosidic attachment through the trisaccharide unit galactosyl-galactosyl-xylosyl. Chondroitin sulfate B is more usually known as dermatan sulfate.
    GO:0050650    chondroitin sulfate proteoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of chondroitin sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Chondroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues; the repeat units consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.
    GO:0050651    dermatan sulfate proteoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of dermatan sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are dermatan sulfate (chondroitin sulfate B). Dermatan sulfate is a glycosaminoglycan with repeats consisting of beta-(1,4)-linked L-iduronyl-beta-(1,3)-N-acetyl-D-galactosamine 4-sulfate units.
    GO:0006024    glycosaminoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
    GO:0030203    glycosaminoglycan metabolic process    The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties.
    GO:0015012    heparan sulfate proteoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues; the former are a mixture of sulfated and nonsulfated D-glucuronic acid and L-iduronic acid; the L-iduronic acid is either sulfated or acetylated on its amino group as well as being sulfated on one of its hydroxyl groups; heparan sulfate chains are covalently linked to peptidyl-serine by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylosyl to serine residues.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0090316    positive regulation of intracellular protein transport    Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells.
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005801    cis-Golgi network    The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts 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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        B3GA3_HUMAN | O947661kws 3cu0

(-) Related Entries Specified in the PDB File

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