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1DIB
Asym. Unit
Info
Asym.Unit (99 KB)
Biol.Unit 1 (94 KB)
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(1)
Title
:
HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE COMPLEXED WITH NADP AND INHIBITOR LY345899
Authors
:
A. Schmidt, H. Wu, R. E. Mackenzie, V. J. Chen, J. R. Bewly, J. E. Ray, J. E. Toth, M. Cygler
Date
:
29 Nov 99 (Deposition) - 05 Jul 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Dehydrogenase, Cyclohydrolase, Nadp, Inhibitor, Rossmann Fold, Oxidoreductase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Schmidt, H. Wu, R. E. Mackenzie, V. J. Chen, J. R. Bewly, J. E. Ray, J. E. Toth, M. Cygler
Structures Of Three Inhibitor Complexes Provide Insight Into The Reaction Mechanism Of The Human Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase.
Biochemistry V. 39 6325 2000
(for further references see the
PDB file header
)
[
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]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: 4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,... (L34a)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
L34
1
Ligand/Ion
4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMIC ACID
2
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
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]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:148 , GLY A:172 , ARG A:173 , SER A:174 , VAL A:177 , HIS A:196 , SER A:197 , THR A:216 , GLN A:218 , MET A:221 , CYS A:236 , GLY A:237 , ILE A:238 , VAL A:275 , GLY A:276 , THR A:279 , L34 A:3001 , HOH A:4001 , HOH A:4059 , HOH A:4101
BINDING SITE FOR RESIDUE NAP A 2001
2
AC2
SOFTWARE
THR B:1148 , VAL B:1171 , GLY B:1172 , ARG B:1173 , SER B:1174 , HIS B:1196 , SER B:1197 , LEU B:1202 , ALA B:1215 , THR B:1216 , GLY B:1217 , GLN B:1218 , MET B:1221 , CYS B:1236 , GLY B:1237 , ILE B:1238 , GLY B:1276 , HOH B:4068
BINDING SITE FOR RESIDUE NAP B 2002
3
AC3
SOFTWARE
TYR A:52 , VAL A:55 , LYS A:56 , LEU A:98 , VAL A:99 , GLN A:100 , LEU A:101 , ASP A:125 , GLY A:273 , GLY A:276 , PRO A:277 , THR A:279 , VAL A:280 , NAP A:2001
BINDING SITE FOR RESIDUE L34 A 3001
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016232 (R1134K, chain A/B, )
2: VAR_055458 (P1162L, chain A/B, )
3: VAR_010241 (R1293H, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016232
R
134
K
C1TC_HUMAN
Polymorphism
1950902
A
B
R
134
1134
K
2
UniProt
VAR_055458
P
162
L
C1TC_HUMAN
Polymorphism
4902283
A
B
P
162
1162
L
3
UniProt
VAR_010241
R
293
H
C1TC_HUMAN
Disease (NTDFS)
34181110
A
B
R
293
1293
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: THF_DHG_CYH_1 (A:78-103,B:1078-1103)
2: THF_DHG_CYH_2 (A:272-280,B:1272-1280)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THF_DHG_CYH_1
PS00766
Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1.
C1TC_HUMAN
78-103
2
A:78-103
B:1078-1103
2
THF_DHG_CYH_2
PS00767
Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2.
C1TC_HUMAN
272-280
2
A:272-280
B:1272-1280
[
close PROSITE info
]
Exons
(10, 20)
Info
All Exons
Exon 1.1 (A:2-14 | B:1002-1014)
Exon 1.2 (A:14-42 | B:1014-1042)
Exon 1.3 (A:43-62 | B:1043-1062)
Exon 1.4 (A:63-80 | B:1063-1080)
Exon 1.5 (A:81-126 | B:1081-1126)
Exon 1.6 (A:126-160 | B:1126-1160)
Exon 1.7 (A:160-205 | B:1160-1205)
Exon 1.8 (A:206-240 | B:1206-1243)
Exon 1.9 (A:251-285 | B:1243-1285)
Exon 1.10 (A:286-296 | B:1286-1296)
View:
Select:
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 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
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
ENST00000216605
1
ENSE00001013539
chr14:
64854958-64855186
229
C1TC_HUMAN
1-14
14
2
A:2-14
B:1002-1014
13
13
1.2
ENST00000216605
2
ENSE00000867603
chr14:
64867511-64867595
85
C1TC_HUMAN
14-42
29
2
A:14-42
B:1014-1042
29
29
1.3
ENST00000216605
3
ENSE00000658402
chr14:
64877808-64877867
60
C1TC_HUMAN
43-62
20
2
A:43-62
B:1043-1062
20
20
1.4
ENST00000216605
4
ENSE00000658403
chr14:
64879190-64879243
54
C1TC_HUMAN
63-80
18
2
A:63-80
B:1063-1080
18
18
1.5
ENST00000216605
5
ENSE00000658404
chr14:
64882076-64882212
137
C1TC_HUMAN
81-126
46
2
A:81-126
B:1081-1126
46
46
1.6
ENST00000216605
6
ENSE00000658405
chr14:
64882357-64882457
101
C1TC_HUMAN
126-160
35
2
A:126-160
B:1126-1160
35
35
1.7
ENST00000216605
7
ENSE00000658406
chr14:
64884606-64884742
137
C1TC_HUMAN
160-205
46
2
A:160-205
B:1160-1205
46
46
1.8
ENST00000216605
8
ENSE00000658407
chr14:
64886532-64886643
112
C1TC_HUMAN
206-243
38
2
A:206-240
B:1206-1243
35
38
1.9
ENST00000216605
9
ENSE00000658408
chr14:
64891522-64891649
128
C1TC_HUMAN
243-285
43
2
A:251-285
B:1243-1285
35
43
1.10
ENST00000216605
10
ENSE00000658409
chr14:
64892448-64892545
98
C1TC_HUMAN
286-318
33
2
A:286-296
B:1286-1296
11
11
1.11
ENST00000216605
11
ENSE00000658410
chr14:
64892737-64892910
174
C1TC_HUMAN
318-376
59
0
-
-
1.12
ENST00000216605
12
ENSE00000658411
chr14:
64894055-64894191
137
C1TC_HUMAN
376-422
47
0
-
-
1.13
ENST00000216605
13
ENSE00000658412
chr14:
64896902-64896948
47
C1TC_HUMAN
422-437
16
0
-
-
1.14
ENST00000216605
14
ENSE00001096762
chr14:
64898250-64898357
108
C1TC_HUMAN
438-473
36
0
-
-
1.15
ENST00000216605
15
ENSE00000658414
chr14:
64898505-64898579
75
C1TC_HUMAN
474-498
25
0
-
-
1.16
ENST00000216605
16
ENSE00001096757
chr14:
64902287-64902389
103
C1TC_HUMAN
499-533
35
0
-
-
1.17
ENST00000216605
17
ENSE00000658416
chr14:
64905814-64905890
77
C1TC_HUMAN
533-558
26
0
-
-
1.18
ENST00000216605
18
ENSE00000658418
chr14:
64906844-64906984
141
C1TC_HUMAN
559-605
47
0
-
-
1.19
ENST00000216605
19
ENSE00000658419
chr14:
64908103-64908171
69
C1TC_HUMAN
606-628
23
0
-
-
1.20
ENST00000216605
20
ENSE00000658420
chr14:
64908772-64908883
112
C1TC_HUMAN
629-666
38
0
-
-
1.21
ENST00000216605
21
ENSE00000658421
chr14:
64908981-64909120
140
C1TC_HUMAN
666-712
47
0
-
-
1.22
ENST00000216605
22
ENSE00000658422
chr14:
64911411-64911452
42
C1TC_HUMAN
713-726
14
0
-
-
1.23
ENST00000216605
23
ENSE00000658423
chr14:
64914935-64915035
101
C1TC_HUMAN
727-760
34
0
-
-
1.24
ENST00000216605
24
ENSE00000658424
chr14:
64916163-64916340
178
C1TC_HUMAN
760-819
60
0
-
-
1.25
ENST00000216605
25
ENSE00000658425
chr14:
64920472-64920579
108
C1TC_HUMAN
820-855
36
0
-
-
1.26
ENST00000216605
26
ENSE00001757563
chr14:
64921441-64921593
153
C1TC_HUMAN
856-906
51
0
-
-
1.27
ENST00000216605
27
ENSE00000867602
chr14:
64924932-64925025
94
C1TC_HUMAN
907-935
29
0
-
-
1.28
ENST00000216605
28
ENSE00001351983
chr14:
64926477-64926721
245
C1TC_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1diba2 (A:2-126)
1b: SCOP_d1dibb2 (B:1002-1126)
2a: SCOP_d1diba1 (A:127-296)
2b: SCOP_d1dibb1 (B:1127-1296)
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Classes
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Folds
(
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(
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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
:
Tetrahydrofolate dehydrogenase/cyclohydrolase
(7)
Protein domain
:
Tetrahydrofolate dehydrogenase/cyclohydrolase
(7)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1diba2
A:2-126
1b
d1dibb2
B:1002-1126
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
:
Methylenetetrahydrofolate dehydrogenase/cyclohydrolase
(7)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d1diba1
A:127-296
2b
d1dibb1
B:1127-1296
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1dibA02 (A:31-119)
1b: CATH_1dibB02 (B:1031-1119)
2a: CATH_1dibB01 (B:1002-1007,B:1146-1276)
2b: CATH_1dibA01 (A:2-7,A:146-276)
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Architectures
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Topologies
(
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(
)
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
1dibA02
A:31-119
1b
1dibB02
B:1031-1119
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
1dibB01
B:1002-1007,B:1146-1276
2b
1dibA01
A:2-7,A:146-276
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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