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3TDK
Asym. Unit
Info
Asym.Unit (1.8 MB)
Biol.Unit 1 (923 KB)
Biol.Unit 2 (927 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN UDP-GLUCOSE DEHYDROGENASE
Authors
:
V. Rajakannan, C. Han, R. Robinson
Date
:
11 Aug 11 (Deposition) - 26 Oct 11 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Open Hexamer, Ugdh, Upg, Nad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Rajakannan, H. S. Lee, S. H. Chong, H. B. Ryu, J. Y. Bae, E. Y. Whang, J. W. Huh, S. W. Cho, L. W. Kang, H. Choe, R. C. Robinson
Structural Basis Of Cooperativity In Human Udp-Glucose Dehydrogenase.
Plos One V. 6 25226 2011
[
close entry info
]
Hetero Components
(2, 24)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
1e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
1g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
1h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
1i: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADi)
1j: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADj)
1k: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADk)
1l: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADl)
2a: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGa)
2b: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGb)
2c: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGc)
2d: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGd)
2e: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGe)
2f: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGf)
2g: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGg)
2h: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGh)
2i: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGi)
2j: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGj)
2k: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGk)
2l: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
12
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
UPG
12
Ligand/Ion
URIDINE-5'-DIPHOSPHATE-GLUCOSE
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:10 , GLY A:13 , TYR A:14 , VAL A:15 , ASP A:36 , VAL A:37 , ARG A:41 , VAL A:89 , ASN A:90 , TYR A:108 , SER A:130 , THR A:131 , VAL A:132 , LYS A:279 , ARG A:346 , HOH A:502
BINDING SITE FOR RESIDUE NAD A 500
02
AC2
SOFTWARE
THR A:131 , GLU A:161 , PHE A:162 , LEU A:163 , ALA A:164 , GLU A:165 , LYS A:220 , ASN A:224 , ILE A:231 , PHE A:265 , LEU A:266 , LYS A:267 , SER A:269 , GLY A:273 , CYS A:276 , PHE A:277 , PHE A:338 , LYS A:339 , ARG A:442 , ARG B:260
BINDING SITE FOR RESIDUE UPG A 501
03
AC3
SOFTWARE
ILE B:10 , GLY B:11 , GLY B:13 , TYR B:14 , VAL B:15 , ASP B:36 , VAL B:37 , ARG B:41 , SER B:88 , VAL B:89 , ASN B:90 , THR B:91 , TYR B:108 , CYS B:112 , SER B:130 , THR B:131 , VAL B:132 , LYS B:279 , ARG B:346
BINDING SITE FOR RESIDUE NAD B 500
04
AC4
SOFTWARE
ARG A:260 , THR B:131 , GLU B:161 , PHE B:162 , LEU B:163 , ALA B:164 , GLU B:165 , LYS B:220 , ASN B:224 , ILE B:231 , PHE B:265 , LEU B:266 , LYS B:267 , SER B:269 , PHE B:272 , GLY B:273 , CYS B:276 , PHE B:277 , PHE B:338 , LYS B:339 , ARG B:442
BINDING SITE FOR RESIDUE UPG B 501
05
AC5
SOFTWARE
ILE G:10 , GLY G:11 , GLY G:13 , TYR G:14 , VAL G:15 , ASP G:36 , VAL G:37 , ARG G:41 , SER G:88 , VAL G:89 , ASN G:90 , THR G:91 , TYR G:108 , SER G:130 , THR G:131 , VAL G:132 , SER G:275 , LYS G:279 , ARG G:346 , HOH G:491 , HOH G:515 , HOH G:533
BINDING SITE FOR RESIDUE NAD G 500
06
AC6
SOFTWARE
THR G:131 , GLU G:161 , PHE G:162 , LEU G:163 , ALA G:164 , GLU G:165 , LYS G:220 , ASN G:224 , ILE G:231 , PHE G:265 , LEU G:266 , LYS G:267 , SER G:269 , PHE G:272 , GLY G:273 , CYS G:276 , PHE G:277 , PHE G:338 , LYS G:339 , ARG G:442 , HOH G:504 , ARG H:260
BINDING SITE FOR RESIDUE UPG G 501
07
AC7
SOFTWARE
ILE H:10 , GLY H:11 , GLY H:13 , TYR H:14 , VAL H:15 , ASP H:36 , ARG H:41 , VAL H:89 , ASN H:90 , THR H:91 , TYR H:108 , SER H:130 , THR H:131 , VAL H:132 , LYS H:279 , ARG H:346 , HOH H:496 , HOH H:520
BINDING SITE FOR RESIDUE NAD H 500
08
AC8
SOFTWARE
ARG G:260 , THR H:131 , GLU H:161 , PHE H:162 , LEU H:163 , ALA H:164 , GLU H:165 , LYS H:220 , ASN H:224 , ILE H:231 , PHE H:265 , LEU H:266 , LYS H:267 , SER H:269 , PHE H:272 , GLY H:273 , CYS H:276 , PHE H:277 , PHE H:338 , LYS H:339 , ARG H:442 , HOH H:508 , HOH H:556 , HOH H:558
BINDING SITE FOR RESIDUE UPG H 501
09
AC9
SOFTWARE
ILE L:10 , GLY L:11 , GLY L:13 , TYR L:14 , VAL L:15 , ASP L:36 , VAL L:37 , ARG L:41 , VAL L:89 , ASN L:90 , THR L:91 , SER L:130 , THR L:131 , VAL L:132 , LYS L:279 , ARG L:346 , HOH L:505
BINDING SITE FOR RESIDUE NAD L 500
10
BC1
SOFTWARE
ARG K:260 , GLU L:161 , PHE L:162 , LEU L:163 , ALA L:164 , GLU L:165 , LYS L:220 , ASN L:224 , LEU L:227 , ILE L:231 , PHE L:265 , LEU L:266 , LYS L:267 , SER L:269 , PHE L:272 , GLY L:273 , CYS L:276 , PHE L:277 , PHE L:338 , LYS L:339 , ARG L:442
BINDING SITE FOR RESIDUE UPG L 501
11
BC2
SOFTWARE
ILE K:10 , GLY K:11 , GLY K:13 , TYR K:14 , VAL K:15 , ASP K:36 , VAL K:37 , ARG K:41 , SER K:88 , VAL K:89 , ASN K:90 , THR K:91 , TYR K:108 , THR K:131 , VAL K:132 , LYS K:279 , ARG K:346
BINDING SITE FOR RESIDUE NAD K 500
12
BC3
SOFTWARE
THR K:131 , GLU K:161 , PHE K:162 , LEU K:163 , ALA K:164 , GLU K:165 , LYS K:220 , ASN K:224 , ILE K:231 , PHE K:265 , LEU K:266 , LYS K:267 , SER K:269 , PHE K:272 , GLY K:273 , CYS K:276 , PHE K:277 , PHE K:338 , LYS K:339 , ARG K:442 , HOH K:493 , ARG L:260
BINDING SITE FOR RESIDUE UPG K 501
13
BC4
SOFTWARE
ARG E:260 , THR F:131 , GLU F:161 , PHE F:162 , LEU F:163 , ALA F:164 , GLU F:165 , LYS F:220 , ILE F:231 , PHE F:265 , LEU F:266 , LYS F:267 , SER F:269 , PHE F:272 , GLY F:273 , CYS F:276 , PHE F:277 , PHE F:338 , LYS F:339 , ARG F:442
BINDING SITE FOR RESIDUE UPG F 501
14
BC5
SOFTWARE
GLY F:11 , GLY F:13 , TYR F:14 , VAL F:15 , ASP F:36 , VAL F:37 , ARG F:41 , VAL F:89 , ASN F:90 , THR F:91 , TYR F:108 , SER F:130 , THR F:131 , VAL F:132 , LYS F:279 , ARG F:346 , HOH F:492
BINDING SITE FOR RESIDUE NAD F 500
15
BC6
SOFTWARE
ILE E:10 , GLY E:11 , ALA E:12 , GLY E:13 , TYR E:14 , VAL E:15 , ASP E:36 , VAL E:37 , ARG E:41 , SER E:88 , VAL E:89 , ASN E:90 , THR E:91 , SER E:130 , THR E:131 , VAL E:132 , LYS E:279 , ARG E:346
BINDING SITE FOR RESIDUE NAD E 500
16
BC7
SOFTWARE
THR E:131 , GLU E:161 , PHE E:162 , LEU E:163 , ALA E:164 , GLU E:165 , LYS E:220 , ASN E:224 , ILE E:231 , PHE E:265 , LEU E:266 , LYS E:267 , SER E:269 , PHE E:272 , GLY E:273 , CYS E:276 , PHE E:277 , PHE E:338 , LYS E:339 , ARG E:442 , ARG F:260
BINDING SITE FOR RESIDUE UPG E 501
17
BC8
SOFTWARE
GLY D:13 , TYR D:14 , VAL D:15 , ASP D:36 , ARG D:41 , VAL D:89 , ASN D:90 , THR D:91 , TYR D:108 , SER D:130 , THR D:131 , VAL D:132 , LYS D:279 , ARG D:346 , HOH D:514 , HOH D:520
BINDING SITE FOR RESIDUE NAD D 500
18
BC9
SOFTWARE
ARG C:260 , THR D:131 , GLU D:161 , PHE D:162 , LEU D:163 , ALA D:164 , GLU D:165 , LYS D:220 , ILE D:231 , PHE D:265 , LEU D:266 , LYS D:267 , SER D:269 , PHE D:272 , GLY D:273 , CYS D:276 , PHE D:277 , PHE D:338 , LYS D:339 , ARG D:442 , HOH D:490
BINDING SITE FOR RESIDUE UPG D 501
19
CC1
SOFTWARE
ILE C:10 , GLY C:11 , GLY C:13 , TYR C:14 , VAL C:15 , ASP C:36 , VAL C:37 , ARG C:41 , SER C:88 , VAL C:89 , ASN C:90 , THR C:91 , CYS C:112 , SER C:130 , THR C:131 , VAL C:132 , LYS C:279 , ARG C:346
BINDING SITE FOR RESIDUE NAD C 500
20
CC2
SOFTWARE
THR C:131 , GLU C:161 , PHE C:162 , LEU C:163 , ALA C:164 , GLU C:165 , LYS C:220 , ASN C:224 , ILE C:231 , PHE C:265 , LEU C:266 , LYS C:267 , SER C:269 , PHE C:272 , GLY C:273 , CYS C:276 , PHE C:277 , PHE C:338 , LYS C:339 , ARG C:442 , HOH C:504 , ARG D:260
BINDING SITE FOR RESIDUE UPG C 501
21
CC3
SOFTWARE
GLY J:11 , GLY J:13 , TYR J:14 , VAL J:15 , ASP J:36 , VAL J:37 , ARG J:41 , VAL J:89 , ASN J:90 , THR J:91 , TYR J:108 , SER J:130 , THR J:131 , VAL J:132 , LYS J:279 , ARG J:346 , HOH J:488
BINDING SITE FOR RESIDUE NAD J 500
22
CC4
SOFTWARE
ARG I:260 , THR J:131 , GLU J:161 , PHE J:162 , LEU J:163 , ALA J:164 , GLU J:165 , LYS J:220 , ASN J:224 , ILE J:231 , PHE J:265 , LEU J:266 , LYS J:267 , SER J:269 , PHE J:272 , GLY J:273 , CYS J:276 , PHE J:277 , PHE J:338 , LYS J:339 , ARG J:442 , HOH J:526
BINDING SITE FOR RESIDUE UPG J 501
23
CC5
SOFTWARE
ILE I:10 , GLY I:11 , GLY I:13 , TYR I:14 , VAL I:15 , ASP I:36 , ARG I:41 , SER I:88 , VAL I:89 , ASN I:90 , THR I:91 , THR I:131 , LYS I:279 , ARG I:346 , HOH I:490
BINDING SITE FOR RESIDUE NAD I 500
24
CC6
SOFTWARE
THR I:131 , GLU I:161 , PHE I:162 , LEU I:163 , ALA I:164 , GLU I:165 , LYS I:220 , ASN I:224 , ILE I:231 , PHE I:265 , LEU I:266 , LYS I:267 , SER I:269 , PHE I:272 , GLY I:273 , CYS I:276 , PHE I:277 , PHE I:338 , LYS I:339 , ARG I:442 , ARG J:260
BINDING SITE FOR RESIDUE UPG I 501
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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
(11, 132)
Info
All Exons
Exon 1.5c (A:1-54 | B:1-54 | C:1-54 | D:1-54 ...)
Exon 1.6b (A:55-88 | B:55-88 | C:55-88 | D:55...)
Exon 1.7f (A:89-155 | B:89-155 | C:89-155 | D...)
Exon 1.8b (A:156-221 | B:156-221 | C:156-221 ...)
Exon 1.9 (A:222-271 | B:222-271 | C:222-271 ...)
Exon 1.10 (A:271-302 | B:271-302 | C:271-302 ...)
Exon 1.11 (A:303-346 | B:303-346 | C:303-346 ...)
Exon 1.12 (A:346-391 (gaps) | B:346-391 (gaps...)
Exon 1.13 (A:391-421 | B:391-421 | C:391-421 ...)
Exon 1.14 (A:422-458 | B:422-458 | C:422-458 ...)
Exon 1.15d (A:459-466 | B:459-466 | C:459-466 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2a/1.5c
02: Boundary 1.5c/1.6b
03: Boundary 1.6b/1.7f
04: Boundary 1.7f/1.8b
05: Boundary 1.8b/1.9
06: Boundary 1.9/1.10
07: Boundary 1.10/1.11
08: Boundary 1.11/1.12
09: Boundary 1.12/1.13
10: Boundary 1.13/1.14
11: Boundary 1.14/1.15d
12: Boundary 1.15d/-
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
1.2a
ENST00000316423
2a
ENSE00001236134
chr4:
39529238-39528903
336
UGDH_HUMAN
-
0
0
-
-
1.5c
ENST00000316423
5c
ENSE00000826500
chr4:
39523139-39522971
169
UGDH_HUMAN
1-54
54
12
A:1-54
B:1-54
C:1-54
D:1-54
E:1-54
F:1-54
G:1-54
H:1-54
I:1-54
J:1-54
K:1-54
L:1-54
54
54
54
54
54
54
54
54
54
54
54
54
1.6b
ENST00000316423
6b
ENSE00000711764
chr4:
39515804-39515703
102
UGDH_HUMAN
55-88
34
12
A:55-88
B:55-88
C:55-88
D:55-88
E:55-88
F:55-88
G:55-88
H:55-88
I:55-88
J:55-88
K:55-88
L:55-88
34
34
34
34
34
34
34
34
34
34
34
34
1.7f
ENST00000316423
7f
ENSE00000711762
chr4:
39512481-39512281
201
UGDH_HUMAN
89-155
67
12
A:89-155
B:89-155
C:89-155
D:89-155
E:89-155
F:89-155
G:89-155
H:89-155
I:89-155
J:89-155
K:89-155
L:89-155
67
67
67
67
67
67
67
67
67
67
67
67
1.8b
ENST00000316423
8b
ENSE00000826499
chr4:
39512170-39511973
198
UGDH_HUMAN
156-221
66
12
A:156-221
B:156-221
C:156-221
D:156-221
E:156-221
F:156-221
G:156-221
H:156-221
I:156-221
J:156-221
K:156-221
L:156-221
66
66
66
66
66
66
66
66
66
66
66
66
1.9
ENST00000316423
9
ENSE00000826498
chr4:
39511527-39511380
148
UGDH_HUMAN
222-271
50
12
A:222-271
B:222-271
C:222-271
D:222-271
E:222-271
F:222-271
G:222-271
H:222-271
I:222-271
J:222-271
K:222-271
L:222-271
50
50
50
50
50
50
50
50
50
50
50
50
1.10
ENST00000316423
10
ENSE00000826497
chr4:
39510280-39510186
95
UGDH_HUMAN
271-302
32
12
A:271-302
B:271-302
C:271-302
D:271-302
E:271-302
F:271-302
G:271-302
H:271-302
I:271-302
J:271-302
K:271-302
L:271-302
32
32
32
32
32
32
32
32
32
32
32
32
1.11
ENST00000316423
11
ENSE00000826496
chr4:
39507368-39507238
131
UGDH_HUMAN
303-346
44
12
A:303-346
B:303-346
C:303-346
D:303-346
E:303-346
F:303-346
G:303-346
H:303-346
I:303-346
J:303-346
K:303-346
L:303-346
44
44
44
44
44
44
44
44
44
44
44
44
1.12
ENST00000316423
12
ENSE00000711745
chr4:
39506990-39506857
134
UGDH_HUMAN
346-391
46
12
A:346-391 (gaps)
B:346-391 (gaps)
C:346-391 (gaps)
D:346-391 (gaps)
E:346-391 (gaps)
F:346-391 (gaps)
G:346-391 (gaps)
H:346-391 (gaps)
I:346-391 (gaps)
J:346-391 (gaps)
K:346-391 (gaps)
L:346-391 (gaps)
46
46
46
46
46
46
46
46
46
46
46
46
1.13
ENST00000316423
13
ENSE00000711741
chr4:
39506128-39506037
92
UGDH_HUMAN
391-421
31
12
A:391-421
B:391-421
C:391-421
D:391-421
E:391-421
F:391-421
G:391-421
H:391-421
I:391-421
J:391-421
K:391-421
L:391-421
31
31
31
31
31
31
31
31
31
31
31
31
1.14
ENST00000316423
14
ENSE00000711736
chr4:
39505605-39505495
111
UGDH_HUMAN
422-458
37
12
A:422-458
B:422-458
C:422-458
D:422-458
E:422-458
F:422-458
G:422-458
H:422-458
I:422-458
J:422-458
K:422-458
L:422-458
37
37
37
37
37
37
37
37
37
37
37
37
1.15d
ENST00000316423
15d
ENSE00001420804
chr4:
39501873-39500375
1499
UGDH_HUMAN
459-494
36
12
A:459-466
B:459-466
C:459-466
D:459-466
E:459-466
F:459-466
G:459-466
H:459-466
I:459-466
J:459-466
K:459-466
L:459-466
8
8
8
8
8
8
8
8
8
8
8
8
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
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by Rainbow (Group)
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (1.8 MB)
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Biol.Unit 1 (923 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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