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1WP4
Asym. Unit
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Asym.Unit (202 KB)
Biol.Unit 1 (197 KB)
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(1)
Title
:
STRUCTURE OF TT368 PROTEIN FROM THERMUS THERMOPHILUS HB8
Authors
:
N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomic Initiative (Rsgi)
Date
:
30 Aug 04 (Deposition) - 30 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Hydroxyisobutyrate, Nadp, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. K. Lokanath, N. Ohshima, K. Takio, I. Shiromizu, C. Kuroishi, N. Okazaki, S. Kuramitsu, S. Yokoyama, M. Miyano, N. Kunishima
Crystal Structure Of Novel Nadp-Dependent 3-Hydroxyisobutyrate Dehydrogenase From Thermus Thermophilu Hb8
J. Mol. Biol. V. 352 905 2005
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
1b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
1c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
1d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(8, 8)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:117 , GLY A:118 , GLY A:119 , LYS A:165 , ASN A:169 , NDP A:1301 , HOH A:1428 , SER B:204
BINDING SITE FOR RESIDUE SO4 A 1305
2
AC2
SOFTWARE
SER A:204 , SER B:117 , GLY B:118 , GLY B:119 , LYS B:165 , ASN B:169 , NDP B:1302 , HOH B:1321 , HOH B:1446
BINDING SITE FOR RESIDUE SO4 B 1306
3
AC3
SOFTWARE
SER C:117 , GLY C:118 , GLY C:119 , LYS C:165 , ASN C:169 , NDP C:1303 , HOH C:1362 , HOH C:1375 , SER D:204
BINDING SITE FOR RESIDUE SO4 C 1307
4
AC4
SOFTWARE
SER D:117 , GLY D:118 , GLY D:119 , LYS D:165 , NDP D:1304 , HOH D:1395 , HOH D:1494
BINDING SITE FOR RESIDUE SO4 D 1308
5
AC5
SOFTWARE
GLY A:8 , LEU A:9 , GLY A:10 , ALA A:11 , MET A:12 , ASN A:30 , ARG A:31 , THR A:32 , LYS A:35 , CYS A:62 , LEU A:63 , PRO A:64 , GLU A:68 , GLU A:71 , THR A:90 , SER A:91 , VAL A:116 , GLY A:119 , LYS A:165 , THR A:226 , PHE A:227 , LYS A:234 , SO4 A:1305 , HOH A:1306 , HOH A:1307 , HOH A:1310 , HOH A:1314 , HOH A:1348 , HOH A:1354 , HOH A:1356 , HOH A:1386 , HOH A:1456 , HOH A:1460
BINDING SITE FOR RESIDUE NDP A 1301
6
AC6
SOFTWARE
GLY C:8 , LEU C:9 , GLY C:10 , ALA C:11 , MET C:12 , ASN C:30 , ARG C:31 , THR C:32 , CYS C:62 , LEU C:63 , PRO C:64 , GLU C:68 , GLU C:71 , SER C:91 , VAL C:116 , GLY C:119 , THR C:226 , PHE C:227 , LYS C:234 , SO4 C:1307 , HOH C:1312 , HOH C:1315 , HOH C:1327 , HOH C:1329 , HOH C:1332 , HOH C:1355 , HOH C:1400 , HOH C:1402 , HOH C:1413 , HOH C:1447 , HOH C:1464 , ARG D:105
BINDING SITE FOR RESIDUE NDP C 1303
7
AC7
SOFTWARE
LEU D:9 , GLY D:10 , ALA D:11 , MET D:12 , ASN D:30 , ARG D:31 , THR D:32 , CYS D:62 , LEU D:63 , PRO D:64 , GLU D:68 , THR D:90 , SER D:91 , VAL D:116 , LYS D:165 , LYS D:234 , SO4 D:1308 , HOH D:1330 , HOH D:1345 , HOH D:1351 , HOH D:1360 , HOH D:1395 , HOH D:1465 , HOH D:1476 , HOH D:1484
BINDING SITE FOR RESIDUE NDP D 1304
8
AC8
SOFTWARE
GLY B:8 , LEU B:9 , GLY B:10 , ALA B:11 , MET B:12 , ASN B:30 , ARG B:31 , THR B:32 , CYS B:62 , LEU B:63 , PRO B:64 , GLU B:68 , GLU B:71 , THR B:90 , SER B:91 , VAL B:116 , GLY B:119 , THR B:226 , PHE B:227 , LYS B:234 , SO4 B:1306 , HOH B:1317 , HOH B:1324 , HOH B:1326 , HOH B:1330 , HOH B:1351 , HOH B:1355 , HOH B:1378
BINDING SITE FOR RESIDUE NDP B 1302
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1wp4a1 (A:158-289)
1b: SCOP_d1wp4b1 (B:158-289)
1c: SCOP_d1wp4c1 (C:158-289)
1d: SCOP_d1wp4d1 (D:158-289)
2a: SCOP_d1wp4a2 (A:2-157)
2b: SCOP_d1wp4b2 (B:2-157)
2c: SCOP_d1wp4c2 (C:2-157)
2d: SCOP_d1wp4d2 (D:2-157)
View:
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(
)
(
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(
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain
(13)
Protein domain
:
Hydroxyisobutyrate dehydrogenase
(5)
Thermus thermophilus [TaxId: 274]
(2)
1a
d1wp4a1
A:158-289
1b
d1wp4b1
B:158-289
1c
d1wp4c1
C:158-289
1d
d1wp4d1
D:158-289
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
:
6-phosphogluconate dehydrogenase-like, N-terminal domain
(69)
Protein domain
:
Hydroxyisobutyrate dehydrogenase
(5)
Thermus thermophilus [TaxId: 274]
(2)
2a
d1wp4a2
A:2-157
2b
d1wp4b2
B:2-157
2c
d1wp4c2
C:2-157
2d
d1wp4d2
D:2-157
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1wp4C01 (C:1-157)
1b: CATH_1wp4D01 (D:1-157)
1c: CATH_1wp4A01 (A:2-157)
1d: CATH_1wp4B01 (B:2-157)
2a: CATH_1wp4A02 (A:158-289)
2b: CATH_1wp4B02 (B:158-289)
2c: CATH_1wp4C02 (C:158-289)
2d: CATH_1wp4D02 (D:158-289)
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)
(
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(8)
1a
1wp4C01
C:1-157
1b
1wp4D01
D:1-157
1c
1wp4A01
A:2-157
1d
1wp4B01
B:2-157
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(60)
Homologous Superfamily
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(59)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(2)
2a
1wp4A02
A:158-289
2b
1wp4B02
B:158-289
2c
1wp4C02
C:158-289
2d
1wp4D02
D:158-289
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_NAD_binding_2_1wp4D01 (D:1-157)
1b: PFAM_NAD_binding_2_1wp4D02 (D:1-157)
1c: PFAM_NAD_binding_2_1wp4D03 (D:1-157)
1d: PFAM_NAD_binding_2_1wp4D04 (D:1-157)
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Clan
:
NADP_Rossmann
(1239)
Family
:
NAD_binding_2
(15)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(1)
1a
NAD_binding_2-1wp4D01
D:1-157
1b
NAD_binding_2-1wp4D02
D:1-157
1c
NAD_binding_2-1wp4D03
D:1-157
1d
NAD_binding_2-1wp4D04
D:1-157
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