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Asym. Unit
Info
Asym.Unit (426 KB)
Biol.Unit 1 (143 KB)
Biol.Unit 2 (144 KB)
Biol.Unit 3 (142 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TRANSHYDROGENASE [(DOMAIN I)2:DOMAIN III] HETEROTRIMER COMPLEX
Authors
:
V. Sundaresan, J. Chartron, M. Yamaguchi, C. D. Stout
Date
:
30 Sep 04 (Deposition) - 05 Apr 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Biol. Unit 3: G,H,I (1x)
Keywords
:
Transhydrogenase, Nad, Nadh, Nadp, Nadph, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Sundaresan, J. Chartron, M. Yamaguchi, C. D. Stout
Conformational Diversity In Nad(H) And Transhydrogenase Nicotinamide Nucleotide Binding Domains
J. Mol. Biol. V. 346 617 2005
(for further references see the
PDB file header
)
[
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]
Hetero Components
(4, 17)
Info
All Hetero Components
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1a: SODIUM ION (NAa)
1b: SODIUM ION (NAb)
1c: SODIUM ION (NAc)
3a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
3b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
3c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
4a: SUCROSE (SUCa)
4b: SUCROSE (SUCb)
4c: SUCROSE (SUCc)
4d: SUCROSE (SUCd)
4e: SUCROSE (SUCe)
4f: SUCROSE (SUCf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
3
Ligand/Ion
SODIUM ION
2
NAD
5
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
NDP
3
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4
SUC
6
Ligand/Ion
SUCROSE
[
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]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:154 , GLU A:155 , PHE A:156 , ALA A:157 , LYS A:316 , ARG B:147 , ARG B:326
BINDING SITE FOR RESIDUE SUC A 600
02
AC2
SOFTWARE
ARG A:147 , ARG A:326 , TYR B:154 , GLU B:155 , LYS B:316
BINDING SITE FOR RESIDUE SUC B 600
03
AC3
SOFTWARE
ASP D:14 , ARG D:147 , ARG D:326 , GLU E:155 , ALA E:157 , LYS E:316
BINDING SITE FOR RESIDUE SUC D 600
04
AC4
SOFTWARE
TYR D:154 , GLU D:155 , ALA D:157 , LYS D:316 , ARG E:147 , ARG E:326
BINDING SITE FOR RESIDUE SUC E 600
05
AC5
SOFTWARE
TYR G:154 , LYS G:316 , ARG H:326
BINDING SITE FOR RESIDUE SUC G 600
06
AC6
SOFTWARE
ARG G:326 , TYR H:154 , GLU H:155 , LYS H:316
BINDING SITE FOR RESIDUE SUC H 600
07
AC7
SOFTWARE
ALA A:159 , PRO A:171 , ASP B:330
BINDING SITE FOR RESIDUE NA A 601
08
AC8
SOFTWARE
ALA D:159 , VAL D:170 , PRO D:171 , ASP E:330
BINDING SITE FOR RESIDUE NA D 602
09
AC9
SOFTWARE
ARG G:158 , ALA G:159 , PRO G:171 , ASP H:330
BINDING SITE FOR RESIDUE NA G 603
10
BC1
SOFTWARE
ARG A:127 , GLN A:132 , ASP A:135 , SER A:138 , VAL A:182 , ASP A:202 , VAL A:203 , ARG A:204 , THR A:264 , ALA A:265 , LEU A:266 , PRO A:273 , LEU A:275
BINDING SITE FOR RESIDUE NAD A 400
11
BC2
SOFTWARE
ARG B:127 , GLY B:179 , GLY B:181 , VAL B:182 , ASP B:202 , ARG B:204 , ALA B:265 , LEU B:266 , ILE B:267 , PRO B:273 , TYR C:432
BINDING SITE FOR RESIDUE NAD B 400
12
BC3
SOFTWARE
GLN B:132 , TYR C:316 , GLY C:317 , VAL C:320 , ALA C:321 , VAL C:348 , ALA C:349 , GLY C:350 , ARG C:351 , MET C:352 , PRO C:353 , GLY C:390 , ALA C:391 , ASN C:392 , ASP C:393 , VAL C:394 , LYS C:425 , ARG C:426 , SER C:427 , SER C:430 , GLY C:431 , TYR C:432 , GLY C:450 , ASP C:451 , ALA C:452
BINDING SITE FOR RESIDUE NDP C 500
13
BC4
SOFTWARE
ARG D:127 , ALA D:131 , GLN D:132 , ASP D:135 , SER D:138 , GLY D:179 , GLY D:181 , VAL D:182 , ASP D:202 , VAL D:203 , ARG D:204 , GLY D:234 , GLN D:247 , THR D:264 , ALA D:265 , LEU D:266 , ILE D:267 , LEU D:275
BINDING SITE FOR RESIDUE NAD D 400
14
BC5
SOFTWARE
SER E:129 , GLN E:132 , GLY F:315 , TYR F:316 , GLY F:317 , ALA F:321 , VAL F:348 , ALA F:349 , GLY F:350 , ARG F:351 , MET F:352 , GLY F:390 , ALA F:391 , ASN F:392 , ASP F:393 , VAL F:394 , MET F:410 , ILE F:424 , LYS F:425 , ARG F:426 , SER F:427 , ALA F:429 , SER F:430 , GLY F:431 , TYR F:432 , ASP F:451 , ALA F:452
BINDING SITE FOR RESIDUE NDP F 500
15
BC6
SOFTWARE
ARG G:127 , ILE G:128 , GLN G:132 , ASP G:135 , GLY G:179 , GLY G:181 , VAL G:182 , ASP G:202 , VAL G:203 , ARG G:204 , THR G:264 , ALA G:265 , LEU G:266 , PRO G:273
BINDING SITE FOR RESIDUE NAD G 400
16
BC7
SOFTWARE
ARG H:127 , ILE H:128 , GLY H:179 , VAL H:180 , GLY H:181 , VAL H:182 , ASP H:202 , VAL H:203 , ARG H:204 , GLN H:210 , ARG H:244 , ALA H:265 , LEU H:266 , ARG I:351 , TYR I:432 , NDP I:500
BINDING SITE FOR RESIDUE NAD H 400
17
BC8
SOFTWARE
GLN H:132 , NAD H:400 , GLY I:315 , TYR I:316 , GLY I:317 , ALA I:321 , VAL I:348 , ALA I:349 , GLY I:350 , ARG I:351 , MET I:352 , GLY I:390 , ALA I:391 , ASN I:392 , ASP I:393 , VAL I:394 , LYS I:425 , ARG I:426 , SER I:427 , GLY I:431 , TYR I:432 , GLY I:450 , ASP I:451 , ALA I:452
BINDING SITE FOR RESIDUE NDP I 500
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: ALADH_PNT_1 (A:4-30,B:4-30,D:4-30,E:4-30,G:4-30...)
2: ALADH_PNT_2 (A:177-202,B:177-202,D:177-202,E:17...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALADH_PNT_1
PS00836
Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1.
PNTAA_RHORT
4-30
6
A:4-30
B:4-30
D:4-30
E:4-30
G:4-30
H:4-30
PNTAA_RHORU
4-30
6
A:4-30
B:4-30
D:4-30
E:4-30
G:4-30
H:4-30
2
ALADH_PNT_2
PS00837
Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2.
PNTAA_RHORT
177-202
6
A:177-202
B:177-202
D:177-202
E:177-202
G:177-202
H:177-202
PNTAA_RHORU
177-202
6
A:177-202
B:177-202
D:177-202
E:177-202
G:177-202
H:177-202
[
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]
Exons
(0, 0)
Info
All Exons
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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
(3, 15)
Info
All SCOP Domains
1a: SCOP_d1xltc_ (C:)
1b: SCOP_d1xltf_ (F:)
1c: SCOP_d1xlti_ (I:)
2a: SCOP_d1xlta2 (A:1-143,A:327-378)
2b: SCOP_d1xltb2 (B:1-143,B:327-378)
2c: SCOP_d1xltd2 (D:1-143,D:327-378)
2d: SCOP_d1xlte2 (E:1-143,E:327-378)
2e: SCOP_d1xltg2 (G:1-143,G:327-378)
2f: SCOP_d1xlth2 (H:1-143,H:327-377)
3a: SCOP_d1xlta1 (A:144-326)
3b: SCOP_d1xltb1 (B:144-326)
3c: SCOP_d1xltd1 (D:144-326)
3d: SCOP_d1xlte1 (E:144-326)
3e: SCOP_d1xltg1 (G:144-326)
3f: SCOP_d1xlth1 (H:144-326)
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)
(
)
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
Transhydrogenase domain III (dIII)
(22)
Protein domain
:
Transhydrogenase domain III (dIII)
(19)
Rhodospirillum rubrum [TaxId: 1085]
(15)
1a
d1xltc_
C:
1b
d1xltf_
F:
1c
d1xlti_
I:
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
L-alanine dehydrogenase-like
(18)
Protein domain
:
Nicotinamide nucleotide transhydrogenase dI component
(15)
Rhodospirillum rubrum [TaxId: 1085]
(15)
2a
d1xlta2
A:1-143,A:327-378
2b
d1xltb2
B:1-143,B:327-378
2c
d1xltd2
D:1-143,D:327-378
2d
d1xlte2
E:1-143,E:327-378
2e
d1xltg2
G:1-143,G:327-378
2f
d1xlth2
H:1-143,H:327-377
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Formate/glycerate dehydrogenases, NAD-domain
(49)
Protein domain
:
Nicotinamide nucleotide transhydrogenase dI component
(15)
Rhodospirillum rubrum [TaxId: 1085]
(15)
3a
d1xlta1
A:144-326
3b
d1xltb1
B:144-326
3c
d1xltd1
D:144-326
3d
d1xlte1
E:144-326
3e
d1xltg1
G:144-326
3f
d1xlth1
H:144-326
[
close SCOP info
]
CATH Domains
(3, 15)
Info
all CATH domains
1a: CATH_1xltA01 (A:2-143,A:327-370)
1b: CATH_1xltB01 (B:2-143,B:327-370)
1c: CATH_1xltD01 (D:2-143,D:327-370)
1d: CATH_1xltE01 (E:2-143,E:327-370)
1e: CATH_1xltG01 (G:2-143,G:327-370)
1f: CATH_1xltH01 (H:2-143,H:327-377)
2a: CATH_1xltD02 (D:144-326)
2b: CATH_1xltG02 (G:144-326)
2c: CATH_1xltA02 (A:144-326)
2d: CATH_1xltE02 (E:144-326)
2e: CATH_1xltH02 (H:144-326)
2f: CATH_1xltB02 (B:144-326)
3a: CATH_1xltF00 (F:292-464)
3b: CATH_1xltI00 (I:292-464)
3c: CATH_1xltC00 (C:291-464)
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Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1770, no name defined]
(22)
Rhodospirillum rubrum. Organism_taxid: 1085.
(11)
1a
1xltA01
A:2-143,A:327-370
1b
1xltB01
B:2-143,B:327-370
1c
1xltD01
D:2-143,D:327-370
1d
1xltE01
E:2-143,E:327-370
1e
1xltG01
G:2-143,G:327-370
1f
1xltH01
H:2-143,H:327-377
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Rhodospirillum rubrum. Organism_taxid: 1085.
(11)
2a
1xltD02
D:144-326
2b
1xltG02
G:144-326
2c
1xltA02
A:144-326
2d
1xltE02
E:144-326
2e
1xltH02
H:144-326
2f
1xltB02
B:144-326
Homologous Superfamily
:
TPP-binding domain
(120)
Rhodospirillum rubrum. Organism_taxid: 1085.
(13)
3a
1xltF00
F:292-464
3b
1xltI00
I:292-464
3c
1xltC00
C:291-464
[
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]
Pfam Domains
(0, 0)
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Asym.Unit (426 KB)
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