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1NR1
Asym. Unit
Info
Asym.Unit (473 KB)
Biol.Unit 1 (468 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE R463A MUTANT OF HUMAN GLUTAMATE DEHYDROGENASE
Authors
:
S. Banerjee, T. Schmidt, J. Fang, C. A. Stanley, T. J. Smith
Date
:
23 Jan 03 (Deposition) - 06 May 03 (Release) - 08 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Glutamate Dehydrogenase, Hexamer, Regulation, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Banerjee, T. Schmidt, J. Fang, C. A. Stanley, T. J. Smith
Structural Studies On Adp Activation Of Mammalian Glutamate Dehydrogenase And The Evolution Of Regulation
Biochemistry V. 42 3446 2003
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Hetero Components
(0, 0)
Info
All Hetero Components
View:
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Label:
Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
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Label:
Sorry, no Info available
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]
SAPs(SNPs)/Variants
(13, 78)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_016760 (S217C, chain A/B/C/D/E/F, )
02: VAR_016761 (R221C, chain A/B/C/D/E/F, )
03: VAR_009270 (R265K, chain A/B/C/D/E/F, )
04: VAR_016762 (R265T, chain A/B/C/D/E/F, )
05: VAR_016763 (Y266C, chain A/B/C/D/E/F, )
06: VAR_016764 (R269C, chain A/B/C/D/E/F, )
07: VAR_016765 (R269H, chain A/B/C/D/E/F, )
08: VAR_009271 (E296A, chain A/B/C/D/E/F, )
09: VAR_008666 (S445L, chain A/B/C/D/E/F, )
10: VAR_008667 (G446D, chain A/B/C/D/E/F, )
11: VAR_008668 (G446S, chain A/B/C/D/E/F, )
12: VAR_008669 (S448P, chain A/B/C/D/E/F, )
13: VAR_008670 (H454Y, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_016760
S
270
C
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
S
217
C
02
UniProt
VAR_016761
R
274
C
DHE3_HUMAN
Disease (HHF6)
56275071
A/B/C/D/E/F
R
221
C
03
UniProt
VAR_009270
R
318
K
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
R
265
K
04
UniProt
VAR_016762
R
318
T
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
R
265
T
05
UniProt
VAR_016763
Y
319
C
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
Y
266
C
06
UniProt
VAR_016764
R
322
C
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
R
269
C
07
UniProt
VAR_016765
R
322
H
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
R
269
H
08
UniProt
VAR_009271
E
349
A
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
E
296
A
09
UniProt
VAR_008666
S
498
L
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
S
445
L
10
UniProt
VAR_008667
G
499
D
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
G
446
D
11
UniProt
VAR_008668
G
499
S
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
G
446
S
12
UniProt
VAR_008669
S
501
P
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
S
448
P
13
UniProt
VAR_008670
H
507
Y
DHE3_HUMAN
Disease (HHF6)
---
A/B/C/D/E/F
H
454
Y
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: GLFV_DEHYDROGENASE (A:124-137,B:124-137,C:124-137,D:12...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLFV_DEHYDROGENASE
PS00074
Glu / Leu / Phe / Val dehydrogenases active site.
DHE3_HUMAN
177-190
6
A:124-137
B:124-137
C:124-137
D:124-137
E:124-137
F:124-137
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Exons
(13, 78)
Info
All Exons
Exon 1.1 (A:10-96 | B:10-96 | C:10-96 | D:10...)
Exon 1.2 (A:96-123 | B:96-123 | C:96-123 | D...)
Exon 1.3 (A:123-141 | B:123-141 | C:123-141 ...)
Exon 1.4 (A:142-163 | B:142-163 | C:142-163 ...)
Exon 1.5 (A:163-194 | B:163-194 | C:163-194 ...)
Exon 1.7 (A:195-254 | B:195-254 | C:195-254 ...)
Exon 1.8b (A:255-300 | B:255-300 | C:255-300 ...)
Exon 1.9a (A:301-346 | B:301-346 | C:301-346 ...)
Exon 1.10b (A:347-373 | B:347-373 | C:347-373 ...)
Exon 1.11 (A:374-415 | B:374-415 | C:374-415 ...)
Exon 1.12b (A:415-445 | B:415-445 | C:415-445 ...)
Exon 1.13 (A:446-466 | B:446-466 | C:446-466 ...)
Exon 1.14 (A:467-505 | B:467-505 | C:467-505 ...)
View:
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Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.7
07: Boundary 1.7/1.8b
08: Boundary 1.8b/1.9a
09: Boundary 1.9a/1.10b
10: Boundary 1.10b/1.11
11: Boundary 1.11/1.12b
12: Boundary 1.12b/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/-
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
ENST00000277865
1
ENSE00000986495
chr10:
88854623-88854082
542
DHE3_HUMAN
1-149
149
6
A:10-96
B:10-96
C:10-96
D:10-96
E:10-96
F:10-96
87
87
87
87
87
87
1.2
ENST00000277865
2
ENSE00001619607
chr10:
88836413-88836333
81
DHE3_HUMAN
149-176
28
6
A:96-123
B:96-123
C:96-123
D:96-123
E:96-123
F:96-123
28
28
28
28
28
28
1.3
ENST00000277865
3
ENSE00001756072
chr10:
88835780-88835725
56
DHE3_HUMAN
176-194
19
6
A:123-141
B:123-141
C:123-141
D:123-141
E:123-141
F:123-141
19
19
19
19
19
19
1.4
ENST00000277865
4
ENSE00001711571
chr10:
88834371-88834308
64
DHE3_HUMAN
195-216
22
6
A:142-163
B:142-163
C:142-163
D:142-163
E:142-163
F:142-163
22
22
22
22
22
22
1.5
ENST00000277865
5
ENSE00000986499
chr10:
88827914-88827820
95
DHE3_HUMAN
216-247
32
6
A:163-194
B:163-194
C:163-194
D:163-194
E:163-194
F:163-194
32
32
32
32
32
32
1.7
ENST00000277865
7
ENSE00000986500
chr10:
88822592-88822413
180
DHE3_HUMAN
248-307
60
6
A:195-254
B:195-254
C:195-254
D:195-254
E:195-254
F:195-254
60
60
60
60
60
60
1.8b
ENST00000277865
8b
ENSE00000986501
chr10:
88820809-88820672
138
DHE3_HUMAN
308-353
46
6
A:255-300
B:255-300
C:255-300
D:255-300
E:255-300
F:255-300
46
46
46
46
46
46
1.9a
ENST00000277865
9a
ENSE00002201813
chr10:
88820582-88820445
138
DHE3_HUMAN
354-399
46
6
A:301-346
B:301-346
C:301-346
D:301-346
E:301-346
F:301-346
46
46
46
46
46
46
1.10b
ENST00000277865
10b
ENSE00001700347
chr10:
88819998-88819918
81
DHE3_HUMAN
400-426
27
6
A:347-373
B:347-373
C:347-373
D:347-373
E:347-373
F:347-373
27
27
27
27
27
27
1.11
ENST00000277865
11
ENSE00001644041
chr10:
88819030-88818907
124
DHE3_HUMAN
427-468
42
6
A:374-415
B:374-415
C:374-415
D:374-415
E:374-415
F:374-415
42
42
42
42
42
42
1.12b
ENST00000277865
12b
ENSE00001791971
chr10:
88817539-88817448
92
DHE3_HUMAN
468-498
31
6
A:415-445
B:415-445
C:415-445
D:415-445
E:415-445
F:415-445
31
31
31
31
31
31
1.13
ENST00000277865
13
ENSE00001717914
chr10:
88813161-88813099
63
DHE3_HUMAN
499-519
21
6
A:446-466
B:446-466
C:446-466
D:446-466
E:446-466
F:446-466
21
21
21
21
21
21
1.14
ENST00000277865
14
ENSE00001777902
chr10:
88811627-88810243
1385
DHE3_HUMAN
520-558
39
6
A:467-505
B:467-505
C:467-505
D:467-505
E:467-505
F:467-505
39
39
39
39
39
39
[
close EXON info
]
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1nr1a2 (A:10-212)
1b: SCOP_d1nr1e2 (E:10-212)
1c: SCOP_d1nr1f2 (F:10-212)
1d: SCOP_d1nr1b2 (B:10-212)
1e: SCOP_d1nr1c2 (C:10-212)
1f: SCOP_d1nr1d2 (D:10-212)
2a: SCOP_d1nr1a1 (A:213-505)
2b: SCOP_d1nr1e1 (E:213-505)
2c: SCOP_d1nr1f1 (F:213-505)
2d: SCOP_d1nr1b1 (B:213-505)
2e: SCOP_d1nr1c1 (C:213-505)
2f: SCOP_d1nr1d1 (D:213-505)
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Aminoacid dehydrogenases
(28)
Protein domain
:
Glutamate dehydrogenase
(19)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1nr1a2
A:10-212
1b
d1nr1e2
E:10-212
1c
d1nr1f2
F:10-212
1d
d1nr1b2
B:10-212
1e
d1nr1c2
C:10-212
1f
d1nr1d2
D:10-212
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Glutamate dehydrogenase
(19)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d1nr1a1
A:213-505
2b
d1nr1e1
E:213-505
2c
d1nr1f1
F:213-505
2d
d1nr1b1
B:213-505
2e
d1nr1c1
C:213-505
2f
d1nr1d1
D:213-505
[
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CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_1nr1A01 (A:61-209)
1b: CATH_1nr1E01 (E:61-209)
1c: CATH_1nr1F01 (F:61-209)
1d: CATH_1nr1B01 (B:61-209)
1e: CATH_1nr1C01 (C:61-209)
1f: CATH_1nr1D01 (D:61-209)
2a: CATH_1nr1A02 (A:210-504)
2b: CATH_1nr1B02 (B:210-504)
2c: CATH_1nr1C02 (C:210-504)
2d: CATH_1nr1D02 (D:210-504)
2e: CATH_1nr1E02 (E:210-504)
2f: CATH_1nr1F02 (F:210-504)
3a: CATH_1nr1A03 (A:10-60)
3b: CATH_1nr1E03 (E:10-60)
3c: CATH_1nr1F03 (F:10-60)
3d: CATH_1nr1B03 (B:10-60)
3e: CATH_1nr1C03 (C:10-60)
3f: CATH_1nr1D03 (D:10-60)
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)
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Architectures
(
)
(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Leucine Dehydrogenase; Chain A, domain 1
(52)
Homologous Superfamily
:
Leucine Dehydrogenase, chain A, domain 1
(52)
Human (Homo sapiens)
(6)
1a
1nr1A01
A:61-209
1b
1nr1E01
E:61-209
1c
1nr1F01
F:61-209
1d
1nr1B01
B:61-209
1e
1nr1C01
C:61-209
1f
1nr1D01
D:61-209
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
1nr1A02
A:210-504
2b
1nr1B02
B:210-504
2c
1nr1C02
C:210-504
2d
1nr1D02
D:210-504
2e
1nr1E02
E:210-504
2f
1nr1F02
F:210-504
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.140, no name defined]
(11)
Human (Homo sapiens)
(2)
3a
1nr1A03
A:10-60
3b
1nr1E03
E:10-60
3c
1nr1F03
F:10-60
3d
1nr1B03
B:10-60
3e
1nr1C03
C:10-60
3f
1nr1D03
D:10-60
[
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]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_ELFV_dehydrog_1nr1F01 (F:210-424)
1b: PFAM_ELFV_dehydrog_1nr1F02 (F:210-424)
1c: PFAM_ELFV_dehydrog_1nr1F03 (F:210-424)
1d: PFAM_ELFV_dehydrog_1nr1F04 (F:210-424)
1e: PFAM_ELFV_dehydrog_1nr1F05 (F:210-424)
1f: PFAM_ELFV_dehydrog_1nr1F06 (F:210-424)
2a: PFAM_ELFV_dehydrog_N_1nr1F07 (F:59-191)
2b: PFAM_ELFV_dehydrog_N_1nr1F08 (F:59-191)
2c: PFAM_ELFV_dehydrog_N_1nr1F09 (F:59-191)
2d: PFAM_ELFV_dehydrog_N_1nr1F10 (F:59-191)
2e: PFAM_ELFV_dehydrog_N_1nr1F11 (F:59-191)
2f: PFAM_ELFV_dehydrog_N_1nr1F12 (F:59-191)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
ELFV_dehydrog
(13)
Homo sapiens (Human)
(2)
1a
ELFV_dehydrog-1nr1F01
F:210-424
1b
ELFV_dehydrog-1nr1F02
F:210-424
1c
ELFV_dehydrog-1nr1F03
F:210-424
1d
ELFV_dehydrog-1nr1F04
F:210-424
1e
ELFV_dehydrog-1nr1F05
F:210-424
1f
ELFV_dehydrog-1nr1F06
F:210-424
Clan
:
no clan defined [family: ELFV_dehydrog_N]
(13)
Family
:
ELFV_dehydrog_N
(13)
Homo sapiens (Human)
(2)
2a
ELFV_dehydrog_N-1nr1F07
F:59-191
2b
ELFV_dehydrog_N-1nr1F08
F:59-191
2c
ELFV_dehydrog_N-1nr1F09
F:59-191
2d
ELFV_dehydrog_N-1nr1F10
F:59-191
2e
ELFV_dehydrog_N-1nr1F11
F:59-191
2f
ELFV_dehydrog_N-1nr1F12
F:59-191
[
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