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1EK6
Asym. Unit
Info
Asym.Unit (138 KB)
Biol.Unit 1 (132 KB)
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(1)
Title
:
STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH NADH AND UDP-GLUCOSE
Authors
:
J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, H. M. Holden
Date
:
06 Mar 00 (Deposition) - 17 May 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Epimerase, Short-Chain Dehydrogenase, Galactosemia, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, H. M. Holden
Crystallographic Evidence For Tyr 157 Functioning As The Active Site Base In Human Udp-Galactose 4-Epimerase.
Biochemistry V. 39 5691 2000
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
2b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
3a: TETRAMETHYLAMMONIUM ION (TMAa)
3b: TETRAMETHYLAMMONIUM ION (TMAb)
3c: TETRAMETHYLAMMONIUM ION (TMAc)
4a: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGa)
4b: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
NAI
2
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3
TMA
3
Ligand/Ion
TETRAMETHYLAMMONIUM ION
4
UPG
2
Ligand/Ion
URIDINE-5'-DIPHOSPHATE-GLUCOSE
[
close Hetero Component info
]
Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:1546 , HOH A:1635 , HOH A:1803 , HOH B:1286 , HOH B:1795 , HOH B:1798
BINDING SITE FOR RESIDUE MG B 960
2
AC2
SOFTWARE
HOH A:1143 , HOH A:1484 , HOH A:1942 , HOH A:1943 , HOH A:1944 , HOH A:1945
BINDING SITE FOR RESIDUE MG A 961
3
AC3
SOFTWARE
GLY A:9 , GLY A:12 , TYR A:13 , ILE A:14 , ASP A:33 , ASN A:34 , HIS A:36 , ASN A:37 , ALA A:38 , MET A:65 , ASP A:66 , ILE A:67 , PHE A:88 , ALA A:89 , GLY A:90 , LYS A:92 , SER A:130 , SER A:131 , SER A:132 , TYR A:157 , LYS A:161 , TYR A:185 , PRO A:188 , UPG A:401 , HOH A:1102 , HOH A:1108 , HOH A:1110 , HOH A:1113 , HOH A:1268 , HOH A:1272 , HOH A:1405
BINDING SITE FOR RESIDUE NAI A 400
4
AC4
SOFTWARE
SER A:132 , THR A:134 , TYR A:157 , PHE A:186 , ASN A:187 , ASN A:206 , ASN A:207 , LEU A:208 , ASN A:224 , VAL A:225 , PHE A:226 , GLY A:237 , ARG A:239 , TYR A:241 , VAL A:277 , ARG A:300 , ASP A:303 , NAI A:400 , HOH A:1114 , HOH A:1127 , HOH A:1195 , HOH A:1199 , HOH A:1485 , HOH A:1496 , HOH A:1511 , HOH A:1532 , HOH A:1666 , HOH A:1791
BINDING SITE FOR RESIDUE UPG A 401
5
AC5
SOFTWARE
GLY B:9 , GLY B:12 , TYR B:13 , ILE B:14 , ASP B:33 , ASN B:34 , PHE B:35 , HIS B:36 , ASN B:37 , ALA B:38 , MET B:65 , ASP B:66 , ILE B:67 , PHE B:88 , ALA B:89 , GLY B:90 , LYS B:92 , SER B:130 , SER B:131 , TYR B:157 , LYS B:161 , TYR B:185 , PHE B:186 , PRO B:188 , UPG B:403 , HOH B:1128 , HOH B:1158 , HOH B:1177 , HOH B:1198 , HOH B:1242 , HOH B:1266 , HOH B:1282 , HOH B:1393
BINDING SITE FOR RESIDUE NAI B 402
6
AC6
SOFTWARE
LYS B:92 , SER B:132 , THR B:134 , TYR B:157 , TYR B:185 , PHE B:186 , ASN B:187 , ASN B:206 , ASN B:207 , LEU B:208 , ASN B:224 , VAL B:225 , PHE B:226 , GLY B:237 , ARG B:239 , TYR B:241 , VAL B:277 , ARG B:300 , ASP B:303 , NAI B:402 , HOH B:1136 , HOH B:1261 , HOH B:1307 , HOH B:1345 , HOH B:1351 , HOH B:1354 , HOH B:1365 , HOH B:1371
BINDING SITE FOR RESIDUE UPG B 403
7
AC7
SOFTWARE
LYS A:257 , GLU A:260 , VAL A:296 , GLU A:317 , HOH A:1274
BINDING SITE FOR RESIDUE TMA A 950
8
AC8
SOFTWARE
HIS B:122 , PRO B:139 , GLN B:140
BINDING SITE FOR RESIDUE TMA B 951
9
AC9
SOFTWARE
MET A:1 , ALA A:25 , GLY A:26
BINDING SITE FOR RESIDUE TMA A 952
[
close Site info
]
SAPs(SNPs)/Variants
(17, 34)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_037733 (A25V, chain A/B, )
02: VAR_002539 (N34S, chain A/B, )
03: VAR_037734 (R40C, chain A/B, )
04: VAR_037735 (D69E, chain A/B, )
05: VAR_002540 (G90E, chain A/B, )
06: VAR_010058 (V94M, chain A/B, )
07: VAR_002541 (D103G, chain A/B, )
08: VAR_037736 (E165K, chain A/B, )
09: VAR_037737 (R169W, chain A/B, )
10: VAR_002542 (A180V, chain A/B, )
11: VAR_002543 (L183P, chain A/B, )
12: VAR_037738 (R239W, chain A/B, )
13: VAR_002544 (K257R, chain A/B, )
14: VAR_037739 (G302D, chain A/B, )
15: VAR_002545 (L313M, chain A/B, )
16: VAR_002546 (G319E, chain A/B, )
17: VAR_037740 (R335H, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_037733
A
25
V
GALE_HUMAN
Disease (EDG)
---
A/B
A
25
V
02
UniProt
VAR_002539
N
34
S
GALE_HUMAN
Disease (EDG)
---
A/B
N
34
S
03
UniProt
VAR_037734
R
40
C
GALE_HUMAN
Disease (EDG)
144492228
A/B
R
40
C
04
UniProt
VAR_037735
D
69
E
GALE_HUMAN
Disease (EDG)
---
A/B
D
69
E
05
UniProt
VAR_002540
G
90
E
GALE_HUMAN
Disease (EDG)
28940882
A/B
G
90
E
06
UniProt
VAR_010058
V
94
M
GALE_HUMAN
Disease (EDG)
---
A/B
V
94
M
07
UniProt
VAR_002541
D
103
G
GALE_HUMAN
Disease (EDG)
28940883
A/B
D
103
G
08
UniProt
VAR_037736
E
165
K
GALE_HUMAN
Disease (EDG)
---
A/B
E
165
K
09
UniProt
VAR_037737
R
169
W
GALE_HUMAN
Disease (EDG)
---
A/B
R
169
W
10
UniProt
VAR_002542
A
180
V
GALE_HUMAN
Polymorphism
3204468
A/B
A
180
V
11
UniProt
VAR_002543
L
183
P
GALE_HUMAN
Disease (EDG)
---
A/B
L
183
P
12
UniProt
VAR_037738
R
239
W
GALE_HUMAN
Disease (EDG)
---
A/B
R
239
W
13
UniProt
VAR_002544
K
257
R
GALE_HUMAN
Disease (EDG)
28940884
A/B
K
257
R
14
UniProt
VAR_037739
G
302
D
GALE_HUMAN
Disease (EDG)
---
A/B
G
302
D
15
UniProt
VAR_002545
L
313
M
GALE_HUMAN
Disease (EDG)
3180383
A/B
L
313
M
16
UniProt
VAR_002546
G
319
E
GALE_HUMAN
Disease (EDG)
28940885
A/B
G
319
E
17
UniProt
VAR_037740
R
335
H
GALE_HUMAN
Disease (EDG)
---
A/B
R
335
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(10, 20)
Info
All Exons
Exon 1.2b (A:1-41 | B:2-41)
Exon 1.2e (A:41-79 | B:41-79)
Exon 1.2h (A:80-117 | B:80-117)
Exon 1.3b (A:118-176 | B:118-176)
Exon 1.4d (A:177-214 | B:177-214)
Exon 1.5 (A:215-237 | B:215-237)
Exon 1.6a (A:237-265 | B:237-265)
Exon 1.6d (A:266-291 | B:266-291)
Exon 1.6e (A:292-330 | B:292-330)
Exon 1.6h (A:330-346 | B:330-346)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1n/1.2b
02: Boundary 1.2b/1.2e
03: Boundary 1.2e/1.2h
04: Boundary 1.2h/1.3b
05: Boundary 1.3b/1.4d
06: Boundary 1.4d/1.5
07: Boundary 1.5/1.6a
08: Boundary 1.6a/1.6d
09: Boundary 1.6d/1.6e
10: Boundary 1.6e/1.6h
11: Boundary 1.6h/-
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
1.1j
ENST00000374497
1j
ENSE00001850298
chr1:
24126892-24126877
16
GALE_HUMAN
-
0
0
-
-
1.1n
ENST00000374497
1n
ENSE00001372948
chr1:
24125926-24125856
71
GALE_HUMAN
-
0
0
-
-
1.2b
ENST00000374497
2b
ENSE00002180266
chr1:
24125502-24125377
126
GALE_HUMAN
1-41
41
2
A:1-41
B:2-41
41
40
1.2e
ENST00000374497
2e
ENSE00001691927
chr1:
24125220-24125105
116
GALE_HUMAN
41-79
39
2
A:41-79
B:41-79
39
39
1.2h
ENST00000374497
2h
ENSE00000758318
chr1:
24124720-24124607
114
GALE_HUMAN
80-117
38
2
A:80-117
B:80-117
38
38
1.3b
ENST00000374497
3b
ENSE00000758319
chr1:
24124361-24124185
177
GALE_HUMAN
118-176
59
2
A:118-176
B:118-176
59
59
1.4d
ENST00000374497
4d
ENSE00000758320
chr1:
24123637-24123524
114
GALE_HUMAN
177-214
38
2
A:177-214
B:177-214
38
38
1.5
ENST00000374497
5
ENSE00000758321
chr1:
24123432-24123366
67
GALE_HUMAN
215-237
23
2
A:215-237
B:215-237
23
23
1.6a
ENST00000374497
6a
ENSE00000758322
chr1:
24123272-24123187
86
GALE_HUMAN
237-265
29
2
A:237-265
B:237-265
29
29
1.6d
ENST00000374497
6d
ENSE00002163869
chr1:
24123076-24122999
78
GALE_HUMAN
266-291
26
2
A:266-291
B:266-291
26
26
1.6e
ENST00000374497
6e
ENSE00002170745
chr1:
24122755-24122641
115
GALE_HUMAN
292-330
39
2
A:292-330
B:292-330
39
39
1.6h
ENST00000374497
6h
ENSE00001893164
chr1:
24122497-24122090
408
GALE_HUMAN
330-348
19
2
A:330-346
B:330-346
17
17
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1ek6a_ (A:)
1b: SCOP_d1ek6b_ (B:)
View:
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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
:
Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)
(26)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1ek6a_
A:
1b
d1ek6b_
B:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1ek6A02 (A:3-189,A:240-270)
1b: CATH_1ek6B02 (B:3-189,B:240-270)
2a: CATH_1ek6A01 (A:190-239,A:271-346)
2b: CATH_1ek6B01 (B:190-239,B:271-346)
View:
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)
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
1ek6A02
A:3-189,A:240-270
1b
1ek6B02
B:3-189,B:240-270
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
1ek6A01
A:190-239,A:271-346
2b
1ek6B01
B:190-239,B:271-346
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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