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1T2A
Asym. Unit
Info
Asym.Unit (253 KB)
Biol.Unit 1 (245 KB)
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(1)
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. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
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
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
1b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
1c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
1d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
2a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
2b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
2c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
2d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDP
4
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
[
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]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
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
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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]
Exons
(11, 44)
Info
All Exons
Exon 1.1 (A:23-34 | B:23-34 | C:23-34 | D:23...)
Exon 1.3 (A:35-49 | B:35-49 | C:35-49 | D:35...)
Exon 1.4 (A:50-79 (gaps) | B:50-79 (gaps) | ...)
Exon 1.5 (A:79-115 | B:79-115 | C:79-115 | D...)
Exon 1.7a (A:116-180 | B:116-180 | C:116-180 ...)
Exon 1.8a (A:180-215 | B:180-215 | C:180-215 ...)
Exon 1.9c (A:215-257 | B:215-257 | C:215-257 ...)
Exon 1.10 (A:258-297 | B:258-297 | C:258-297 ...)
Exon 1.11a (A:297-329 | B:297-329 | C:297-329 ...)
Exon 1.17 (A:330-352 | B:330-352 | C:330-352 ...)
Exon 1.18b (A:353-369 | B:353-369 | C:353-369 ...)
View:
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All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.7a
06: Boundary 1.7a/1.8a
07: Boundary 1.8a/1.9c
08: Boundary 1.9c/1.10
09: Boundary 1.10/1.11a
10: Boundary 1.11a/1.17
11: Boundary 1.17/1.18b
12: Boundary 1.18b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1t2aa_ (A:)
1b: SCOP_d1t2ab_ (B:)
1c: SCOP_d1t2ac_ (C:)
1d: SCOP_d1t2ad_ (D:)
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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:
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1t2aA01 (A:23-214,A:250-277,A:329-349)
1b: CATH_1t2aB01 (B:23-214,B:250-277,B:329-349)
1c: CATH_1t2aC01 (C:23-214,C:250-277,C:329-349)
1d: CATH_1t2aD01 (D:23-214,D:250-277,D:329-349)
2a: CATH_1t2aA02 (A:215-249,A:278-328,A:350-369)
2b: CATH_1t2aB02 (B:215-249,B:278-328,B:350-369)
2c: CATH_1t2aC02 (C:215-249,C:278-328,C:350-369)
2d: CATH_1t2aD02 (D:215-249,D:278-328,D:350-368)
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)
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
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Epimerase_1t2aD01 (D:26-274)
1b: PFAM_Epimerase_1t2aD02 (D:26-274)
1c: PFAM_Epimerase_1t2aD03 (D:26-274)
1d: PFAM_Epimerase_1t2aD04 (D:26-274)
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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
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