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(-) Description

Title :  CRYSTAL STRUCTURE OF GTB C80S/C196S + DA + UDP-GAL
 
Authors :  B. Schuman, M. Persson, R. C. Landry, R. Polakowski, J. T. Weadge, N. O. L S. Borisova, M. M. Palcic, S. V. Evans
Date :  25 Jun 09  (Deposition) - 11 Aug 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Gtb, Glycosyltransferase, Abo Blood Group, Retaining, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Schuman, M. Persson, R. C. Landry, R. Polakowski, J. T. Weadge, N. O. Seto, S. N. Borisova, M. M. Palcic, S. V. Evans
Cysteine-To-Serine Mutants Dramatically Reorder The Active Site Of Human Abo(H) Blood Group B Glycosyltransferase Without Affecting Activity: Structural Insights Into Cooperative Substrate Binding
J. Mol. Biol. V. 402 399 2010
PubMed-ID: 20655926  |  Reference-DOI: 10.1016/J.JMB.2010.07.036

(-) Compounds

Molecule 1 - ABO GLYCOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCW(DELTA)LAC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 59 TO 344
    Gene: GTB
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1BHG1Ligand/Ion2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4MN1Ligand/IonMANGANESE (II) ION
5UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1BHG2Ligand/Ion2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4MN-1Ligand/IonMANGANESE (II) ION
5UDP4Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:57 , HIS A:233 , SER A:235 , PHE A:236 , THR A:245 , TYR A:264 , TRP A:300 , GLU A:303 , FUC A:356 , UDP A:358 , HOH A:402BINDING SITE FOR RESIDUE BHG A 1
2AC2SOFTWAREBHG A:1 , MET A:266 , ASP A:326 , UDP A:358 , HOH A:393 , HOH A:402 , HOH A:448 , HOH A:476BINDING SITE FOR RESIDUE FUC A 356
3AC3SOFTWAREASP A:211 , ASP A:213 , UDP A:358 , HOH A:366 , HOH A:378 , HOH A:422BINDING SITE FOR RESIDUE MN A 2
4AC4SOFTWAREHOH A:8 , HOH A:40 , HOH A:58 , SER A:80 , LEU A:85 , PRO A:89 , GLY A:98 , THR A:99 , PHE A:100 , ASN A:101 , HOH A:387 , HOH A:444 , HOH A:472 , HOH A:563 , HOH A:629BINDING SITE FOR RESIDUE UDP A 357
5AC5SOFTWAREBHG A:1 , MN A:2 , HOH A:22 , HOH A:25 , PHE A:121 , ALA A:122 , ILE A:123 , TYR A:126 , ASP A:211 , VAL A:212 , ASP A:213 , FUC A:356 , GAL A:359 , HOH A:401 , HOH A:413 , HOH A:451 , HOH A:471 , HOH A:502BINDING SITE FOR RESIDUE UDP A 358
6AC6SOFTWAREHOH A:22 , ARG A:188 , GLY A:267 , TRP A:300 , HIS A:301 , ASP A:302 , GLU A:303 , UDP A:358 , HOH A:471BINDING SITE FOR RESIDUE GAL A 359

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I0G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:175 -Gly A:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (20, 20)

Asymmetric Unit (20, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_019150P74SBGAT_HUMANPolymorphism512770AP74S
02UniProtVAR_003409P156LBGAT_HUMANPolymorphism1053878AP156L
03UniProtVAR_019151R161HBGAT_HUMANPolymorphism8176738AR161H
04UniProtVAR_036738T163MBGAT_HUMANPolymorphism55756402AT163M
05UniProtVAR_003410R176GBGAT_HUMANPolymorphism7853989AG176G
06UniProtVAR_036739R198WBGAT_HUMANPolymorphism56223957AR198W
07UniProtVAR_019152R199CBGAT_HUMANPolymorphism8176739AR199C
08UniProtVAR_036740M214RBGAT_HUMANPolymorphism55827808AM214R
09UniProtVAR_019153F216IBGAT_HUMANPolymorphism8176740AF216I
10UniProtVAR_036741E223DBGAT_HUMANPolymorphism  ---AE223D
11UniProtVAR_055227G230RBGAT_HUMANUnclassified  ---AG230R
12UniProtVAR_072628P234ABGAT_HUMANPolymorphism  ---AP234A
13UniProtVAR_003411G235SBGAT_HUMANPolymorphism8176743AS235S
14UniProtVAR_033540P257LBGAT_HUMANPolymorphism8176745AP257L
15UniProtVAR_003412L266MBGAT_HUMANPolymorphism8176746AM266M
16UniProtVAR_003413G268ABGAT_HUMANPolymorphism8176747AA268A
17UniProtVAR_033541G268RBGAT_HUMANPolymorphism8176747AA268R
18UniProtVAR_019154V277MBGAT_HUMANPolymorphism8176748AV277M
19UniProtVAR_036742M288RBGAT_HUMANPolymorphism  ---AM288R
20UniProtVAR_036743D291NBGAT_HUMANPolymorphism  ---AD291N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (20, 40)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_019150P74SBGAT_HUMANPolymorphism512770AP74S
02UniProtVAR_003409P156LBGAT_HUMANPolymorphism1053878AP156L
03UniProtVAR_019151R161HBGAT_HUMANPolymorphism8176738AR161H
04UniProtVAR_036738T163MBGAT_HUMANPolymorphism55756402AT163M
05UniProtVAR_003410R176GBGAT_HUMANPolymorphism7853989AG176G
06UniProtVAR_036739R198WBGAT_HUMANPolymorphism56223957AR198W
07UniProtVAR_019152R199CBGAT_HUMANPolymorphism8176739AR199C
08UniProtVAR_036740M214RBGAT_HUMANPolymorphism55827808AM214R
09UniProtVAR_019153F216IBGAT_HUMANPolymorphism8176740AF216I
10UniProtVAR_036741E223DBGAT_HUMANPolymorphism  ---AE223D
11UniProtVAR_055227G230RBGAT_HUMANUnclassified  ---AG230R
12UniProtVAR_072628P234ABGAT_HUMANPolymorphism  ---AP234A
13UniProtVAR_003411G235SBGAT_HUMANPolymorphism8176743AS235S
14UniProtVAR_033540P257LBGAT_HUMANPolymorphism8176745AP257L
15UniProtVAR_003412L266MBGAT_HUMANPolymorphism8176746AM266M
16UniProtVAR_003413G268ABGAT_HUMANPolymorphism8176747AA268A
17UniProtVAR_033541G268RBGAT_HUMANPolymorphism8176747AA268R
18UniProtVAR_019154V277MBGAT_HUMANPolymorphism8176748AV277M
19UniProtVAR_036742M288RBGAT_HUMANPolymorphism  ---AM288R
20UniProtVAR_036743D291NBGAT_HUMANPolymorphism  ---AD291N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I0G)

(-) Exons   (0, 0)

(no "Exon" information available for 3I0G)

(-) 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:268
 aligned with BGAT_HUMAN | P16442 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:276
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339      
           BGAT_HUMAN    70 VYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVRAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPGFYGSSREAFTYERRPQSQAYIPKDEGDFYYLGGFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVP 345
               SCOP domains d3i0ga_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................ee.....hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhh........eeeeeee..--------.hhhhhhhhhhhhhhhhh...eeeee...eee....hhhhh..eeee........hhhhh........................eeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eee.hhhh.hhhhhh.........eee.. Sec.struct. author
             SAPs(SNPs) (1) ----S---------------------------------------------------------------------------------L----H-M------------G---------------------WC--------------R-I------D------R---AS---------------------L--------M-A--------M----------R--N------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3i0g A  70 VYPQPKVLTPSRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVG--------SMRRMEMISDFSERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPSFYGSSREAFTYERRPQSQAYIPKDEGDFYYMGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVP 345
                                    79        89        99       109       119       129       139       149       159       169      |  -     | 189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339      
                                                                                                                                    176      185                                                                                                                                                                


Chain A from PDB  Type:PROTEIN  Length:268
 aligned with Q70V26_HUMAN | Q70V26 from UniProtKB/TrEMBL  Length:344

    Alignment length:276
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329      
         Q70V26_HUMAN    60 VYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVGAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPSFYGSSREAFTYERRPQSQAYIPKDEGDFYYMGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVP 335
               SCOP domains d3i0ga_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................ee.....hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhh........eeeeeee..--------.hhhhhhhhhhhhhhhhh...eeeee...eee....hhhhh..eeee........hhhhh........................eeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eee.hhhh.hhhhhh.........eee.. Sec.struct. author
             SAPs(SNPs) (1) ----S---------------------------------------------------------------------------------L----H-M------------G---------------------WC--------------R-I------D------R---AS---------------------L--------M-A--------M----------R--N------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3i0g A  70 VYPQPKVLTPSRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVG--------SMRRMEMISDFSERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPSFYGSSREAFTYERRPQSQAYIPKDEGDFYYMGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVP 345
                                    79        89        99       109       119       129       139       149       159       169      |  -     | 189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339      
                                                                                                                                    176      185
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I0G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I0G)

(-) Gene Ontology  (13, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (BGAT_HUMAN | P16442)
molecular function
    GO:0004381    fucosylgalactoside 3-alpha-galactosyltransferase activity    Catalysis of the reaction: UDP-galactose + glycoprotein-alpha-L-fucosyl-(1,2)-D-galactose = UDP + glycoprotein-alpha-D-galactosyl-(1,3)-(alpha-L-fucosyl-(1,2))-D-galactose.
    GO:0004380    glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity    Catalysis of the reaction: UDP-N-acetyl-D-galactosamine + glycoprotein-alpha-L-fucosyl-(1,2)-D-galactose = UDP + glycoprotein-N-acetyl-alpha-D-galactosaminyl-(1,3)-(alpha-L-fucosyl-(1,2))-D-galactose.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016758    transferase activity, transferring hexosyl groups    Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
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: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:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    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: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.

Chain A   (Q70V26_HUMAN | Q70V26)
molecular function
    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.
    GO:0016758    transferase activity, transferring hexosyl groups    Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
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.
cellular component
    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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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BGAT_HUMAN | P16442: 1lz0 1lz7 1lzi 1lzj 1r7t 1r7u 1r7v 1r7x 1r7y 1r80 1r81 1r82 1wsz 1wt0 1wt1 1wt2 1wt3 1xz6 1zhj 1zi1 1zi3 1zi4 1zi5 1ziz 1zj0 1zj1 1zj2 1zj3 1zjo 1zjp 2a8u 2a8w 2i7b 2o1f 2o1g 2o1h 2pgv 2pgy 2rit 2rix 2riy 2riz 2rj0 2rj1 2rj4 2rj5 2rj6 2rj7 2rj8 2rj9 2y7a 3i0c 3i0d 3i0e 3i0f 3i0h 3i0i 3i0j 3i0k 3i0l 3ioh 3ioi 3ioj 3sx3 3sx5 3sx7 3sx8 3sxa 3sxb 3sxc 3sxd 3sxe 3sxg 3u0x 3u0y 3v0l 3v0m 3v0n 3v0o 3v0p 3v0q 3zgf 3zgg 4c2s 4fqw 4fra 4frb 4frd 4fre 4frh 4frl 4frm 4fro 4frp 4frq 4gbp 4kc1 4kc2 4kc4 4kxo 4y62 4y63 4y64 5bxc 5c1g 5c1h 5c1l 5c36 5c38 5c3a 5c3b 5c3d 5c47 5c48 5c49 5c4b 5c4c 5c4d 5c4e 5c4f 5c8r 5cmf 5cmg 5cmh 5cmi 5cmj 5cql 5cqm 5cqn 5cqo 5cqp 5tjk 5tjl 5tjn 5tjo
        Q70V26_HUMAN | Q70V26: 2y7a 3i0c 3i0d 3i0e 3i0f 3i0h 3i0i 3i0j 3i0k 3i0l

(-) Related Entries Specified in the PDB File

1lz7 GTB
3i0c GTB C80S/C196S UNLIGANDED
3i0d GTB C80S/C196S + UDP
3i0e GTB C80S/C196S + H ANTIGEN
3i0f GTB C80S/C196S + UDP + H ANTIGEN
3i0h GTB C80S/C196S/C209S UNLIGANDED
3i0i GTB C80S/C196S/C209S + UDP
3i0j GTB C80S/C196S/C209S + H ANTIGEN
3i0k GTB C80S/C196S/C209S + UDP + H ANTIGEN
3i0l GTB C80S/C196S/C209S + DA + UDP-GAL