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(-) Description

Title :  CRYSTAL STRUCTURE OF GDP-MANNOSE 4,6 DEHYDRATASE BOUND TO A GDP-FUCOSE BASED INHIBITOR
 
Authors :  E. A. Sickmier
Date :  07 Mar 16  (Deposition) - 17 Aug 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Gdp-Mannose 4, 6 Dehydratase, Antibody Fucosylation, Lyase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Allen, M. Mujacic, M. J. Frohn, A. J. Pickrell, P. Kodama, D. Bagal T. San Miguel, E. A. Sickmier, S. Osgood, A. Swietlow, V. Li, J. B. Jordan, K. W. Kim, A. C. Rousseau, Y. J. Kim, S. Caille, M. Achmatowicz, O. Thiel, C. H. Fotsch, P. Reddy, J. D. Mccarter
Facile Modulation Of Antibody Fucosylation With Small Molecule Fucostatin Inhibitors And Cocrystal Structure With Gdp-Mannose 4, 6-Dehydratase.
Acs Chem. Biol. V. 11 2734 2016
PubMed-ID: 27434622  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00460

(-) Compounds

Molecule 1 - GDP-MANNOSE 4,6 DEHYDRATASE
    Chains: A, B, C, D
    EC Number: 4.2.1.47
    Engineered: YES
    Expression System: ENTEROBACTERIA PHAGE L1
    Expression System Taxid: 268588
    Gene: GMDS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GDP-D-MANNOSE DEHYDRATASE,GMD

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
16CK4Ligand/Ion[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4R,5S,6R)-3,4,5-TRIHYDROXY-6-(TRIFLUOROMETHYL)TETRAHYDRO-2H-PYRAN-2-YL DIHYDROGEN DIPHOSPHATE (NON-PREFERRED NAME)
2GDP4Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:30 , THR A:32 , GLY A:33 , GLN A:34 , ASP A:35 , ARG A:55 , ASN A:61 , ASP A:86 , LEU A:87 , LEU A:108 , GLY A:109 , ALA A:110 , SER A:112 , TYR A:123 , VAL A:127 , ALA A:153 , SER A:154 , THR A:155 , TYR A:179 , LYS A:183 , LEU A:206 , ASN A:208 , HIS A:209 , ARG A:214 , HOH A:1108 , HOH A:1183 , HOH A:1212 , HOH A:1213 , HOH A:1214 , HOH A:1217 , HOH A:1234 , HOH A:1253 , HOH A:1255 , HOH A:1282 , HOH A:1310 , HOH A:1319 , HOH A:1328 , ARG B:56 , SER B:57 , SER B:58 , HOH B:711binding site for residue NAP A 1001
02AC2SOFTWAREVAL A:114 , GLU A:157 , ASN A:208 , ASN A:217 , PHE A:218 , VAL A:219 , LYS A:222 , LEU A:240 , GLY A:241 , ASN A:242 , ALA A:245 , ARG A:247 , VAL A:281 , TYR A:323 , ARG A:325 , GLU A:328 , HOH A:1130 , HOH A:1161 , HOH A:1260 , HOH A:1266 , HOH B:574binding site for residue GDP A 1002
03AC3SOFTWAREPHE A:60 , THR A:62 , TYR A:69 , HIS A:75 , GLU A:77 , LEU A:82 , TYR A:84 , HOH A:1112 , HOH A:1153 , HOH A:1167 , HOH A:1178 , HOH A:1197 , HOH A:1211 , HOH A:1224 , HOH A:1237 , ALA B:216 , ASN B:217 , LYS B:222 , ARG B:225 , TYR B:323 , ALA B:372binding site for residue 6CK A 1003
04AC4SOFTWAREALA A:216 , ASN A:217 , LYS A:222 , ARG A:225 , TYR A:323 , ALA A:372 , VAL B:54 , PHE B:60 , THR B:62 , TYR B:69 , HIS B:75 , GLU B:77 , LEU B:82 , TYR B:84 , HOH B:510 , HOH B:574 , HOH B:580 , HOH B:582 , HOH B:593 , HOH B:622 , HOH B:629 , HOH B:659 , HOH B:668 , HOH B:739 , HOH B:746binding site for residue 6CK B 401
05AC5SOFTWAREARG A:56 , SER A:57 , SER A:58 , HOH A:1209 , GLY B:30 , THR B:32 , GLY B:33 , GLN B:34 , ASP B:35 , ARG B:55 , ASN B:61 , ASP B:86 , LEU B:87 , LEU B:108 , GLY B:109 , ALA B:110 , SER B:112 , TYR B:123 , VAL B:127 , ALA B:153 , SER B:154 , THR B:155 , TYR B:179 , LYS B:183 , LEU B:206 , ASN B:208 , HIS B:209 , ARG B:214 , HOH B:528 , HOH B:602 , HOH B:605 , HOH B:619 , HOH B:652 , HOH B:658 , HOH B:660 , HOH B:674 , HOH B:688 , HOH B:702 , HOH B:726binding site for residue NAP B 402
06AC6SOFTWAREHOH A:1178 , VAL B:114 , GLU B:157 , ASN B:208 , ASN B:217 , PHE B:218 , VAL B:219 , LYS B:222 , LEU B:240 , GLY B:241 , ASN B:242 , ALA B:245 , ARG B:247 , VAL B:281 , TYR B:323 , ARG B:325 , GLU B:328 , HOH B:522 , HOH B:525 , HOH B:527 , HOH B:531 , HOH B:620 , HOH B:654binding site for residue GDP B 403
07AC7SOFTWAREGLY C:30 , THR C:32 , GLY C:33 , GLN C:34 , ASP C:35 , ARG C:55 , ASN C:61 , ASP C:86 , LEU C:87 , LEU C:108 , GLY C:109 , ALA C:110 , SER C:112 , TYR C:123 , VAL C:127 , ALA C:153 , SER C:154 , THR C:155 , TYR C:179 , LYS C:183 , LEU C:206 , ASN C:208 , HIS C:209 , ARG C:214 , HOH C:1141 , HOH C:1148 , HOH C:1193 , HOH C:1226 , HOH C:1255 , HOH C:1257 , HOH C:1264 , HOH C:1273 , HOH C:1281 , HOH C:1283 , HOH C:1285 , HOH C:1336 , ARG D:56 , SER D:57 , SER D:58 , HOH D:754binding site for residue NAP C 1001
08AC8SOFTWAREVAL C:114 , GLU C:157 , ASN C:208 , ASN C:217 , PHE C:218 , VAL C:219 , LYS C:222 , LEU C:240 , GLY C:241 , ASN C:242 , ALA C:245 , ARG C:247 , VAL C:281 , TYR C:323 , ARG C:325 , GLU C:328 , HOH C:1115 , HOH C:1220 , HOH C:1270 , HOH C:1277 , HOH C:1344 , HOH D:584binding site for residue GDP C 1002
09AC9SOFTWAREPHE C:60 , THR C:62 , TYR C:69 , HIS C:75 , GLU C:77 , LEU C:82 , TYR C:84 , HOH C:1113 , HOH C:1144 , HOH C:1149 , HOH C:1196 , HOH C:1239 , HOH C:1242 , HOH C:1244 , HOH C:1340 , HOH C:1352 , HOH C:1356 , ALA D:216 , ASN D:217 , LYS D:222 , ARG D:225 , TYR D:323 , ALA D:372 , HOH D:626binding site for residue 6CK C 1003
10AD1SOFTWAREALA C:216 , ASN C:217 , LYS C:222 , ARG C:225 , TYR C:323 , ALA C:372 , PHE D:60 , THR D:62 , TYR D:69 , HIS D:75 , GLU D:77 , LEU D:82 , TYR D:84 , HOH D:527 , HOH D:556 , HOH D:570 , HOH D:584 , HOH D:594 , HOH D:625 , HOH D:647 , HOH D:675 , HOH D:689 , HOH D:781binding site for residue 6CK D 401
11AD2SOFTWAREARG C:56 , SER C:57 , SER C:58 , HOH C:1136 , GLY D:30 , THR D:32 , GLY D:33 , GLN D:34 , ASP D:35 , ARG D:55 , ASN D:61 , ASP D:86 , LEU D:87 , LEU D:108 , GLY D:109 , ALA D:110 , SER D:112 , TYR D:123 , VAL D:127 , ALA D:153 , SER D:154 , THR D:155 , TYR D:179 , LYS D:183 , LEU D:206 , ASN D:208 , HIS D:209 , ARG D:214 , HOH D:558 , HOH D:571 , HOH D:595 , HOH D:634 , HOH D:643 , HOH D:659 , HOH D:672 , HOH D:680 , HOH D:692 , HOH D:724 , HOH D:732 , HOH D:764binding site for residue NAP D 402
12AD3SOFTWAREVAL D:114 , GLU D:157 , ASN D:208 , ASN D:217 , PHE D:218 , VAL D:219 , LYS D:222 , LEU D:240 , GLY D:241 , ASN D:242 , ALA D:245 , ARG D:247 , VAL D:281 , TYR D:323 , ARG D:325 , GLU D:328 , HOH D:559 , HOH D:569 , HOH D:626 , HOH D:687 , HOH D:695 , HOH D:715binding site for residue GDP D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IN4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:165 -Pro A:166
2Ile B:165 -Pro B:166
3Ile C:165 -Pro C:166
4Ile D:165 -Pro D:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IN4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IN4)

(-) Exons   (0, 0)

(no "Exon" information available for 5IN4)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee..........hhhhh..........eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....eee.eehhhhhhhhhhhhhh.....eee....eeehhhhhhhhhhh....eeee.hhhh.eeee.....eeeee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5in4 A -26 LYFQGRNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPNA 372
                                ||  27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367     
                              -22|                                                                                                                                                                                                                                                                                                                                                             
                                23                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee..........hhhhh..........eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhh.................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....ee..eehhhhhhhhhhhhhh.....eee.....eehhhhhhhhhhhh...eeee.hhhhheeee.....eeeee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5in4 B -22 GRNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPNA 372
                            ||      31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371 
                          -22|                                                                                                                                                                                                                                                                                                                                                             
                            23                                                                                                                                                                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee..........hhhhh..........eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....ee..eehhhhhhhhhhhhhh.....eee.....eehhhhhhhhhhhh...eeee.hhhh.eeee.....eeeee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5in4 C -22 GRNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPNA 372
                            ||      31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371 
                          -22|                                                                                                                                                                                                                                                                                                                                                             
                            23                                                                                                                                                                                                                                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee..........hhhhh..........eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....ee..eehhhhhhhhhhhhhh.....eee.....eehhhhhhhhhhh....eeee.hhhhheeee.....eeeee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5in4 D -22 GRNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPNA 372
                            ||      31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371 
                          -22|                                                                                                                                                                                                                                                                                                                                                             
                            23
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

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(no "SCOP Domain" information available for 5IN4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IN4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IN4)

(-) Gene Ontology  (10, 10)

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 Related Entries

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        GMDS_HUMAN | O60547: 1t2a 5in5

(-) Related Entries Specified in the PDB File

5in5