1T2A - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN GDP-D-MANNOSE 4,6-DEHYDRATASE

Authors :   J. R. Walker, M. Vedadi, S. Sharma, S. Houston, G. Wasney, P. Loppnau, M. Sundstrom, C. Arrowsmith, A. Edwards, U. Oppermann

Date :   20 Apr 04 (Deposition) - 10 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Structural Genomics Consortium, Rossman-Fold, Short-Chain Dehydrogenase/Reductase, Sdr, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Vedadi, J. R. Walker, S. Sharma, S. Houston, G. Wasney, P. Loppnau, U. Oppermann
Crystal Structure And Biophysical Characterization Of Human Gdp-D-Mannose 4, 6-Dehydratase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GDP-MANNOSE 4,6 DEHYDRATASE
	Chains	:	A, B, C, D
	EC Number	:	4.2.1.47
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GMDS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GDP-D-MANNOSE DEHYDRATASE, GMD

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	GDP	4	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:30 , THR A:32 , GLY A:33 , GLN A:34 , ASP A:35 , ARG A:55 , 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:1004 , HOH A:1010 , HOH A:1013 , HOH A:1015 , HOH A:1017 , HOH A:1021 , HOH A:1031 , HOH A:1039 , HOH A:1059 , HOH A:1071 , HOH A:1147 , HOH A:1190 , ARG D:56 , SER D:57 , SER D:58 , HOH D:1320	BINDING SITE FOR RESIDUE NDP A 1001
2	AC2	SOFTWARE	VAL A:114 , 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:1011 , HOH A:1036 , HOH A:1042 , HOH A:1045 , HOH A:1046 , HOH A:1064 , HOH A:1174	BINDING SITE FOR RESIDUE GDP A 1002
3	AC3	SOFTWARE	GLY B:30 , THR B:32 , GLY B:33 , GLN B:34 , ASP B:35 , ARG B:55 , 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:1111 , HOH B:1113 , HOH B:1119 , HOH B:1128 , HOH B:1131 , HOH B:1132 , HOH B:1152 , HOH B:1196 , HOH B:1256 , HOH B:1271 , HOH B:1341 , ARG C:56 , SER C:58 , HOH C:1244	BINDING SITE FOR RESIDUE NDP B 1101
4	AC4	SOFTWARE	HIS B:113 , GLU B:157 , ASN B:208 , ASN B:217 , VAL B:219 , LYS B:222 , LEU B:240 , GLY B:241 , ASN B:242 , ALA B:245 , ARG B:247 , VAL B:281 , ARG B:325 , GLU B:328 , HOH B:1109 , HOH B:1122 , HOH B:1129 , HOH B:1133 , HOH B:1223 , HOH B:1274	BINDING SITE FOR RESIDUE GDP B 1102
5	AC5	SOFTWARE	ARG B:56 , SER B:57 , SER B:58 , GLY C:30 , THR C:32 , GLY C:33 , GLN C:34 , ASP C:35 , ARG C:55 , 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:1205 , HOH C:1206 , HOH C:1210 , HOH C:1211 , HOH C:1213 , HOH C:1217 , HOH C:1227 , HOH C:1230 , HOH C:1235 , HOH C:1316 , HOH C:1341 , HOH C:1344 , HOH C:1345	BINDING SITE FOR RESIDUE NDP C 1201
6	AC6	SOFTWARE	VAL C:114 , GLU C:157 , ASN C:208 , ASN C:217 , 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:1226 , HOH C:1232 , HOH C:1236 , HOH C:1241 , HOH C:1250 , HOH C:1300 , HOH C:1334	BINDING SITE FOR RESIDUE GDP C 1202
7	AC7	SOFTWARE	ARG A:56 , SER A:57 , SER A:58 , HOH A:1205 , GLY D:30 , THR D:32 , GLY D:33 , GLN D:34 , ASP D:35 , ARG D:55 , 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:1303 , HOH D:1304 , HOH D:1307 , HOH D:1316 , HOH D:1321 , HOH D:1330 , HOH D:1343 , HOH D:1344 , HOH D:1345 , HOH D:1367 , HOH D:1461 , HOH D:1483	BINDING SITE FOR RESIDUE NDP D 1301
8	AC8	SOFTWARE	HIS D:113 , VAL 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:1312 , HOH D:1317 , HOH D:1318 , HOH D:1327 , HOH D:1348 , HOH D:1376 , HOH D:1425	BINDING SITE FOR RESIDUE GDP D 1302

(no "SS Bond" information available for 1T2A)

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 1T2A)

(no "PROSITE Motif" information available for 1T2A)

Asymmetric/Biological Unit (11, 44)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000380815	1	ENSE00001486507	chr6:2245926-2245555	372	GMDS_HUMAN	1-34	34	4	A:23-34 B:23-34 C:23-34 D:23-34	12 12 12 12
1.3	ENST00000380815	3	ENSE00000973296	chr6:2124965-2124921	45	GMDS_HUMAN	35-49	15	4	A:35-49 B:35-49 C:35-49 D:35-49	15 15 15 15
1.4	ENST00000380815	4	ENSE00000973297	chr6:2117790-2117703	88	GMDS_HUMAN	50-79	30	4	A:50-79 (gaps) B:50-79 (gaps) C:50-79 (gaps) D:50-79 (gaps)	30 30 30 30
1.5	ENST00000380815	5	ENSE00000973298	chr6:2116114-2116005	110	GMDS_HUMAN	79-115	37	4	A:79-115 B:79-115 C:79-115 D:79-115	37 37 37 37
1.7a	ENST00000380815	7a	ENSE00000680356	chr6:1961200-1961008	193	GMDS_HUMAN	116-180	65	4	A:116-180 B:116-180 C:116-180 D:116-180	65 65 65 65
1.8a	ENST00000380815	8a	ENSE00001161320	chr6:1960205-1960101	105	GMDS_HUMAN	180-215	36	4	A:180-215 B:180-215 C:180-215 D:180-215	36 36 36 36
1.9c	ENST00000380815	9c	ENSE00000680236	chr6:1930464-1930337	128	GMDS_HUMAN	215-257	43	4	A:215-257 B:215-257 C:215-257 D:215-257	43 43 43 43
1.10	ENST00000380815	10	ENSE00001983509	chr6:1742820-1742702	119	GMDS_HUMAN	258-297	40	4	A:258-297 B:258-297 C:258-297 D:258-297	40 40 40 40
1.11a	ENST00000380815	11a	ENSE00000973273	chr6:1726746-1726650	97	GMDS_HUMAN	297-329	33	4	A:297-329 B:297-329 C:297-329 D:297-329	33 33 33 33
1.17	ENST00000380815	17	ENSE00001978182	chr6:1624775-1624707	69	GMDS_HUMAN	330-352	23	4	A:330-352 B:330-352 C:330-352 D:330-352	23 23 23 23
1.18b	ENST00000380815	18b	ENSE00001976024	chr6:1624466-1624041	426	GMDS_HUMAN	353-372	20	4	A:353-369 B:353-369 C:353-369 D:353-368	17 17 17 16

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:338
 aligned with GMDS_HUMAN | O60547 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:347
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
           GMDS_HUMAN    23 RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTN 369
               SCOP domains d1t2aa_ A: GDP-mannose 4,6-dehydratase                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1t2aA01 A:23-214,A:250-277,A:329-349 NAD(P)-bin         ding Rossmann-like Domain                                                                                                               1t2aA02                            1t2aA01                     1t2aA02 A:215-249,A:278-328,A:350-369              1t2aA01              1t2aA02              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.hhhh.eeee.....eeeee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1    Exon 1.3       Exon 1.4  PDB: A:50-79 (gaps) ------------------------------------Exon 1.7a  PDB: A:116-180 UniProt: 116-180                       ----------------------------------Exon 1.9c  PDB: A:215-257 UniProt: 215-257 Exon 1.10  PDB: A:258-297               --------------------------------Exon 1.17              Exon 1.18b        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.5  PDB: A:79-115              ----------------------------------------------------------------Exon 1.8a  PDB: A:180-215           ---------------------------------------------------------------------------------Exon 1.11a  PDB: A:297-329       ---------------------------------------- Transcript 1 (2)
                 1t2a A  23 RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLY---------NMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTN 369
                                    32        42        52        62      |  -      | 82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
                                                                         69        79

Chain B from PDB  Type:PROTEIN  Length:338
 aligned with GMDS_HUMAN | O60547 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:347
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
           GMDS_HUMAN    23 RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTN 369
               SCOP domains d1t2ab_ B: GDP-mannose 4,6-dehydratase                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1t2aB01 B:23-214,B:250-277,B:329-349 NAD(P)-bin         ding Rossmann-like Domain                                                                                                               1t2aB02                            1t2aB01                     1t2aB02 B:215-249,B:278-328,B:350-369              1t2aB01              1t2aB02              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.hhhh.eeee.....eeeee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1    Exon 1.3       Exon 1.4  PDB: B:50-79 (gaps) ------------------------------------Exon 1.7a  PDB: B:116-180 UniProt: 116-180                       ----------------------------------Exon 1.9c  PDB: B:215-257 UniProt: 215-257 Exon 1.10  PDB: B:258-297               --------------------------------Exon 1.17              Exon 1.18b        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.5  PDB: B:79-115              ----------------------------------------------------------------Exon 1.8a  PDB: B:180-215           ---------------------------------------------------------------------------------Exon 1.11a  PDB: B:297-329       ---------------------------------------- Transcript 1 (2)
                 1t2a B  23 RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLY---------NMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTN 369
                                    32        42        52        62      |  -      | 82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
                                                                         69        79

Chain C from PDB  Type:PROTEIN  Length:338
 aligned with GMDS_HUMAN | O60547 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:347
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
           GMDS_HUMAN    23 RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTN 369
               SCOP domains d1t2ac_ C: GDP-mannose 4,6-dehydratase                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1t2aC01 C:23-214,C:250-277,C:329-349 NAD(P)-bin         ding Rossmann-like Domain                                                                                                               1t2aC02                            1t2aC01                     1t2aC02 C:215-249,C:278-328,C:350-369              1t2aC01              1t2aC02              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.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1    Exon 1.3       Exon 1.4  PDB: C:50-79 (gaps) ------------------------------------Exon 1.7a  PDB: C:116-180 UniProt: 116-180                       ----------------------------------Exon 1.9c  PDB: C:215-257 UniProt: 215-257 Exon 1.10  PDB: C:258-297               --------------------------------Exon 1.17              Exon 1.18b        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.5  PDB: C:79-115              ----------------------------------------------------------------Exon 1.8a  PDB: C:180-215           ---------------------------------------------------------------------------------Exon 1.11a  PDB: C:297-329       ---------------------------------------- Transcript 1 (2)
                 1t2a C  23 RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLY---------NMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTN 369
                                    32        42        52        62      |  -      | 82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
                                                                         69        79

Chain D from PDB  Type:PROTEIN  Length:337
 aligned with GMDS_HUMAN | O60547 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:346
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
           GMDS_HUMAN    23 RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRT 368
               SCOP domains d1t2ad_ D: GDP-mannose 4,6-dehydratase                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1t2aD01 D:23-214,D:250-277,D:329-349 NAD(P)-bin         ding Rossmann-like Domain                                                                                                               1t2aD02                            1t2aD01                     1t2aD02 D:215-249,D:278-328,D:350-368              1t2aD01              1t2aD02             CATH domains
           Pfam domains (1) ---Epimerase-1t2aD01 D:26-274                                                                                                                                                                                                                               ---------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Epimerase-1t2aD02 D:26-274                                                                                                                                                                                                                               ---------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---Epimerase-1t2aD03 D:26-274                                                                                                                                                                                                                               ---------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---Epimerase-1t2aD04 D:26-274                                                                                                                                                                                                                               ---------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee..........hhhhh---------.eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....ee..eehhhhhhhhhhhhhh.....eee.....eehhhhhhhhhhh....eeee.hhhh.eeee.....eeeee.hhhh...........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1    Exon 1.3       Exon 1.4  PDB: D:50-79 (gaps) ------------------------------------Exon 1.7a  PDB: D:116-180 UniProt: 116-180                       ----------------------------------Exon 1.9c  PDB: D:215-257 UniProt: 215-257 Exon 1.10  PDB: D:258-297               --------------------------------Exon 1.17              Exon 1.18b       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.5  PDB: D:79-115              ----------------------------------------------------------------Exon 1.8a  PDB: D:180-215           ---------------------------------------------------------------------------------Exon 1.11a  PDB: D:297-329       --------------------------------------- Transcript 1 (2)
                 1t2a D  23 RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLY---------NMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRT 368
                                    32        42        52        62      |  -      | 82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
                                                                         69        79

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: GDP-mannose 4,6-dehydratase (5)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1t2aa_	A:
1b	d1t2ab_	B:
1c	d1t2ac_	C:
1d	d1t2ad_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Human (Homo sapiens) (188)

1a	1t2aA01	A:23-214,A:250-277,A:329-349
1b	1t2aB01	B:23-214,B:250-277,B:329-349
1c	1t2aC01	C:23-214,C:250-277,C:329-349
1d	1t2aD01	D:23-214,D:250-277,D:329-349

Architecture: Alpha-Beta Complex (3881)

Topology: UDP-galactose 4-epimerase; domain 1 (99)

Homologous Superfamily: UDP-galactose 4-epimerase, domain 1 (99)

Human (Homo sapiens) (8)

2a	1t2aA02	A:215-249,A:278-328,A:350-369
2b	1t2aB02	B:215-249,B:278-328,B:350-369
2c	1t2aC02	C:215-249,C:278-328,C:350-369
2d	1t2aD02	D:215-249,D:278-328,D:350-368

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Epimerase (42)

Homo sapiens (Human) (1)

1a	Epimerase-1t2aD01	D:26-274
1b	Epimerase-1t2aD02	D:26-274
1c	Epimerase-1t2aD03	D:26-274
1d	Epimerase-1t2aD04	D:26-274

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (GMDS_HUMAN | O60547)

molecular function
	GO:0008446	GDP-mannose 4,6-dehydratase activity	Catalysis of the reaction: GDP-alpha-D-mannose = GDP-4-dehydro-6-deoxy-alpha-D-mannose + H(2)O.
	GO:0070401	NADP+ binding	Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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).
biological process
	GO:0042351	'de novo' GDP-L-fucose biosynthetic process	The chemical reactions and pathways resulting in the formation of GDP-L-fucose from GDP-D-mannose via GDP-4-dehydro-6-deoxy-D-mannose, requiring the functions of GDP-mannose 4,6-dehydratase (EC:4.2.1.47) and GDP-L-fucose synthase (EC:1.1.1.271).
	GO:0019673	GDP-mannose metabolic process	The chemical reactions and pathways involving GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
	GO:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:165 - Pro A:166	[ RasMol ]
		Ile B:165 - Pro B:166	[ RasMol ]
		Ile C:165 - Pro C:166	[ RasMol ]
		Ile D:165 - Pro D:166	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1t2a
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GMDS_HUMAN \| O60547
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.2.1.47
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GMDS_HUMAN \| O60547
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GMDS_HUMAN \| O60547	:	5in4 5in5

(no "Related Entries Specified in the PDB File" available for 1T2A)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (11, 44)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (2, 8)

Pfam Domains (1, 4)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File