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3PRJ
Asym. Unit
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Asym.Unit (452 KB)
Biol.Unit 1 (442 KB)
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(1)
Title
:
ROLE OF PACKING DEFECTS IN THE EVOLUTION OF ALLOSTERY AND INDUCED FIT IN HUMAN UDP-GLUCOSE DEHYDROGENASE.
Authors
:
R. Kadirvelraj, Z. A. Wood
Date
:
29 Nov 10 (Deposition) - 15 Jun 11 (Release) - 24 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Feedback Inhibition, Rossmann Fold, Nucleotide Sugar Dehydrogenase, Nad Binding, Cytosol, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Kadirvelraj, N. C. Sennett, S. J. Polizzi, S. Weitzel, Z. A. Wood
Role Of Packing Defects In The Evolution Of Allostery And Induced Fit In Human Udp-Glucose Dehydrogenase.
Biochemistry V. 50 5780 2011
[
close entry info
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
1b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
1c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
1d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
1e: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIe)
1f: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIf)
2a: URIDINE-5'-DIPHOSPHATE-XYLOPYRANOS... (UDXa)
2b: URIDINE-5'-DIPHOSPHATE-XYLOPYRANOS... (UDXb)
2c: URIDINE-5'-DIPHOSPHATE-XYLOPYRANOS... (UDXc)
2d: URIDINE-5'-DIPHOSPHATE-XYLOPYRANOS... (UDXd)
2e: URIDINE-5'-DIPHOSPHATE-XYLOPYRANOS... (UDXe)
2f: URIDINE-5'-DIPHOSPHATE-XYLOPYRANOS... (UDXf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAI
6
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2
UDX
6
Ligand/Ion
URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE
[
close Hetero Component info
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:10 , GLY A:11 , GLY A:13 , TYR A:14 , VAL A:15 , ASP A:36 , VAL A:37 , ARG A:41 , VAL A:89 , ASN A:90 , THR A:91 , SER A:130 , THR A:131 , VAL A:132 , SER A:275 , LYS A:279 , ARG A:346 , HOH A:504
BINDING SITE FOR RESIDUE NAI 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 , ILE A:231 , PHE A:265 , LEU A:266 , LYS A:267 , SER A:269 , PHE A:272 , 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 UDX A 501
03
AC3
SOFTWARE
GLY B:11 , GLY B:13 , TYR B:14 , VAL B:15 , ASP B:36 , VAL B:37 , ARG B:41 , VAL B:89 , ASN B:90 , THR B:91 , CYS B:112 , SER B:130 , THR B:131 , VAL B:132 , SER B:275 , LYS B:279 , ARG B:346
BINDING SITE FOR RESIDUE NAI 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 UDX B 501
05
AC5
SOFTWARE
ILE C:10 , GLY C:13 , TYR C:14 , VAL C:15 , ASP C:36 , VAL C:37 , ARG C:41 , VAL C:89 , ASN C:90 , THR C:91 , PRO C:92 , SER C:130 , THR C:131 , VAL C:132 , LYS C:279 , ARG C:346
BINDING SITE FOR RESIDUE NAI C 500
06
AC6
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 , 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 , ARG D:260
BINDING SITE FOR RESIDUE UDX C 501
07
AC7
SOFTWARE
ILE D:10 , GLY D:11 , GLY D:13 , TYR D:14 , VAL D:15 , ASP D:36 , VAL D:37 , ARG D:41 , VAL D:89 , ASN D:90 , THR D:91 , SER D:130 , THR D:131 , VAL D:132 , SER D:275 , LYS D:279 , ARG D:346
BINDING SITE FOR RESIDUE NAI D 500
08
AC8
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 , PHE D:265 , 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
BINDING SITE FOR RESIDUE UDX D 501
09
AC9
SOFTWARE
ILE E:10 , GLY E:11 , GLY E:13 , TYR E:14 , VAL E:15 , ASP E:36 , VAL E:37 , ARG E:41 , VAL E:89 , ASN E:90 , SER E:130 , THR E:131 , VAL E:132 , SER E:275 , LYS E:279 , ARG E:346
BINDING SITE FOR RESIDUE NAI E 500
10
BC1
SOFTWARE
THR E:131 , GLU E:161 , PHE E:162 , LEU E:163 , ALA E:164 , GLU E:165 , LYS E:220 , ILE E:231 , PHE E:265 , 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 UDX E 501
11
BC2
SOFTWARE
ILE F:10 , 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 , SER F:275 , LYS F:279 , ARG F:346 , HOH F:503
BINDING SITE FOR RESIDUE NAI F 500
12
BC3
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 , 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 UDX F 501
[
close Site info
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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
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;
View:
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End label:
Sorry, no Info available
[
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]
Exons
(11, 66)
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:
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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
6
A:1-54
B:1-54
C:1-54
D:1-54
E:1-54
F:1-54
54
54
54
54
54
54
1.6b
ENST00000316423
6b
ENSE00000711764
chr4:
39515804-39515703
102
UGDH_HUMAN
55-88
34
6
A:55-88
B:55-88
C:55-88
D:55-88
E:55-88
F:55-88
34
34
34
34
34
34
1.7f
ENST00000316423
7f
ENSE00000711762
chr4:
39512481-39512281
201
UGDH_HUMAN
89-155
67
6
A:89-155
B:89-155
C:89-155
D:89-155
E:89-155
F:89-155
67
67
67
67
67
67
1.8b
ENST00000316423
8b
ENSE00000826499
chr4:
39512170-39511973
198
UGDH_HUMAN
156-221
66
6
A:156-221
B:156-221
C:156-221
D:156-221
E:156-221
F:156-221
66
66
66
66
66
66
1.9
ENST00000316423
9
ENSE00000826498
chr4:
39511527-39511380
148
UGDH_HUMAN
222-271
50
6
A:222-271
B:222-271
C:222-271
D:222-271
E:222-271
F:222-271
50
50
50
50
50
50
1.10
ENST00000316423
10
ENSE00000826497
chr4:
39510280-39510186
95
UGDH_HUMAN
271-302
32
6
A:271-302
B:271-302
C:271-302
D:271-302
E:271-302
F:271-302
32
32
32
32
32
32
1.11
ENST00000316423
11
ENSE00000826496
chr4:
39507368-39507238
131
UGDH_HUMAN
303-346
44
6
A:303-346
B:303-346
C:303-346
D:303-346
E:303-346
F:303-346
44
44
44
44
44
44
1.12
ENST00000316423
12
ENSE00000711745
chr4:
39506990-39506857
134
UGDH_HUMAN
346-391
46
6
A:346-391 (gaps)
B:346-391 (gaps)
C:346-391 (gaps)
D:346-391 (gaps)
E:346-391 (gaps)
F:346-391 (gaps)
46
46
46
46
46
46
1.13
ENST00000316423
13
ENSE00000711741
chr4:
39506128-39506037
92
UGDH_HUMAN
391-421
31
6
A:391-421
B:391-421
C:391-421
D:391-421
E:391-421
F:391-421
31
31
31
31
31
31
1.14
ENST00000316423
14
ENSE00000711736
chr4:
39505605-39505495
111
UGDH_HUMAN
422-458
37
6
A:422-458
B:422-458
C:422-458
D:422-458
E:422-458
F:422-458
37
37
37
37
37
37
1.15d
ENST00000316423
15d
ENSE00001420804
chr4:
39501873-39500375
1499
UGDH_HUMAN
459-494
36
6
A:459-466
B:459-466
C:459-466
D:459-465
E:459-466
F:459-466
8
8
8
7
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
[
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Pfam Domains
(3, 18)
Info
all PFAM domains
1a: PFAM_UDPG_MGDP_dh_3prjF01 (F:213-310)
1b: PFAM_UDPG_MGDP_dh_3prjF02 (F:213-310)
1c: PFAM_UDPG_MGDP_dh_3prjF03 (F:213-310)
1d: PFAM_UDPG_MGDP_dh_3prjF04 (F:213-310)
1e: PFAM_UDPG_MGDP_dh_3prjF05 (F:213-310)
1f: PFAM_UDPG_MGDP_dh_3prjF06 (F:213-310)
2a: PFAM_UDPG_MGDP_dh_N_3prjF07 (F:5-195)
2b: PFAM_UDPG_MGDP_dh_N_3prjF08 (F:5-195)
2c: PFAM_UDPG_MGDP_dh_N_3prjF09 (F:5-195)
2d: PFAM_UDPG_MGDP_dh_N_3prjF10 (F:5-195)
2e: PFAM_UDPG_MGDP_dh_N_3prjF11 (F:5-195)
2f: PFAM_UDPG_MGDP_dh_N_3prjF12 (F:5-195)
3a: PFAM_UDPG_MGDP_dh_C_3prjF13 (F:332-447)
3b: PFAM_UDPG_MGDP_dh_C_3prjF14 (F:332-447)
3c: PFAM_UDPG_MGDP_dh_C_3prjF15 (F:332-447)
3d: PFAM_UDPG_MGDP_dh_C_3prjF16 (F:332-447)
3e: PFAM_UDPG_MGDP_dh_C_3prjF17 (F:332-447)
3f: PFAM_UDPG_MGDP_dh_C_3prjF18 (F:332-447)
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Clan
:
6PGD_C
(47)
Family
:
UDPG_MGDP_dh
(10)
Homo sapiens (Human)
(5)
1a
UDPG_MGDP_dh-3prjF01
F:213-310
1b
UDPG_MGDP_dh-3prjF02
F:213-310
1c
UDPG_MGDP_dh-3prjF03
F:213-310
1d
UDPG_MGDP_dh-3prjF04
F:213-310
1e
UDPG_MGDP_dh-3prjF05
F:213-310
1f
UDPG_MGDP_dh-3prjF06
F:213-310
Clan
:
NADP_Rossmann
(1239)
Family
:
UDPG_MGDP_dh_N
(10)
Homo sapiens (Human)
(5)
2a
UDPG_MGDP_dh_N-3prjF07
F:5-195
2b
UDPG_MGDP_dh_N-3prjF08
F:5-195
2c
UDPG_MGDP_dh_N-3prjF09
F:5-195
2d
UDPG_MGDP_dh_N-3prjF10
F:5-195
2e
UDPG_MGDP_dh_N-3prjF11
F:5-195
2f
UDPG_MGDP_dh_N-3prjF12
F:5-195
Clan
:
no clan defined [family: UDPG_MGDP_dh_C]
(10)
Family
:
UDPG_MGDP_dh_C
(10)
Homo sapiens (Human)
(5)
3a
UDPG_MGDP_dh_C-3prjF13
F:332-447
3b
UDPG_MGDP_dh_C-3prjF14
F:332-447
3c
UDPG_MGDP_dh_C-3prjF15
F:332-447
3d
UDPG_MGDP_dh_C-3prjF16
F:332-447
3e
UDPG_MGDP_dh_C-3prjF17
F:332-447
3f
UDPG_MGDP_dh_C-3prjF18
F:332-447
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