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2OO5
Asym. Unit
Info
Asym.Unit (264 KB)
Biol.Unit 1 (257 KB)
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(1)
Title
:
STRUCTURE OF TRANSHYDROGENASE (DI.H2NADH)2(DIII.NADP+)1 ASYMMETRIC COMPLEX
Authors
:
T. Bhakta, J. B. Jackson
Date
:
25 Jan 07 (Deposition) - 13 Mar 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Rossmann Fold; Nad(H)-Binding Site; Nadp(H)-Binding Site, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Bhakta, S. J. Whitehead, J. S. Snaith, T. R. Dafforn, J. Wilkie, S. Rajesh, S. A. White, J. B. Jackson
Structures Of The Di(2)Diii(1) Complex Of Proton-Translocating Transhydrogenase With Bound, Inactive Analogues Of Nadh And Nadph Reveal Active Site Geometries
Biochemistry V. 46 3304 2007
(for further references see the
PDB file header
)
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
3a: 1,4,5,6-TETRAHYDRONICOTINAMIDE ADE... (TXDa)
3b: 1,4,5,6-TETRAHYDRONICOTINAMIDE ADE... (TXDb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
NAP
1
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2
SO4
4
Ligand/Ion
SULFATE ION
3
TXD
2
Ligand/Ion
1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:147 , ARG A:326 , TYR B:154
BINDING SITE FOR RESIDUE SO4 B 385
2
AC2
SOFTWARE
THR A:169 , PRO A:171 , SO4 A:386 , ASP B:330 , PRO B:333
BINDING SITE FOR RESIDUE SO4 B 386
3
AC3
SOFTWARE
TYR A:154 , LYS A:316 , ARG B:147 , ARG B:326
BINDING SITE FOR RESIDUE SO4 A 385
4
AC4
SOFTWARE
ARG A:158 , HOH A:501 , HOH A:510 , PRO B:333 , SO4 B:386
BINDING SITE FOR RESIDUE SO4 A 386
5
AC5
SOFTWARE
SER B:129 , TXD B:600 , GLY C:54 , TYR C:55 , GLY C:56 , ALA C:60 , VAL C:87 , GLY C:89 , ARG C:90 , MET C:91 , PRO C:92 , GLY C:129 , ALA C:130 , ASN C:131 , ASP C:132 , VAL C:133 , LYS C:164 , ARG C:165 , SER C:166 , GLY C:170 , TYR C:171 , GLY C:189 , ASP C:190 , ALA C:191
BINDING SITE FOR RESIDUE NAP C 400
6
AC6
SOFTWARE
ARG A:127 , ILE A:128 , GLN A:132 , ASP A:135 , GLY A:179 , GLY A:181 , VAL A:182 , ASP A:202 , VAL A:203 , ARG A:204 , GLY A:234 , ALA A:236 , GLN A:247 , THR A:264 , ALA A:265 , LEU A:266 , PRO A:273 , LEU A:275
BINDING SITE FOR RESIDUE TXD A 500
7
AC7
SOFTWARE
ARG B:127 , ILE B:128 , SER B:129 , GLN B:132 , SER B:138 , GLY B:179 , VAL B:180 , GLY B:181 , VAL B:182 , ASP B:202 , VAL B:203 , ARG B:204 , GLY B:234 , TYR B:235 , ALA B:236 , GLN B:247 , THR B:264 , ALA B:265 , LEU B:266 , PRO B:273 , LEU B:275 , HOH B:607 , TYR C:171 , NAP C:400
BINDING SITE FOR RESIDUE TXD B 600
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ALADH_PNT_1 (A:4-30,B:4-30,A:4-30,B:4-30)
2: ALADH_PNT_2 (A:177-202,B:177-202,A:177-202,B:17...)
;
View:
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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
2
A:4-30
B:4-30
PNTAA_RHORU
4-30
2
A:4-30
B:4-30
2
ALADH_PNT_2
PS00837
Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2.
PNTAA_RHORT
177-202
2
A:177-202
B:177-202
PNTAA_RHORU
177-202
2
A:177-202
B:177-202
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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
(3, 5)
Info
All SCOP Domains
1a: SCOP_d2oo5c_ (C:)
2a: SCOP_d2oo5a2 (A:1-143,A:327-380)
2b: SCOP_d2oo5b2 (B:1-143,B:327-380)
3a: SCOP_d2oo5a1 (A:144-326)
3b: SCOP_d2oo5b1 (B:144-326)
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)
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)
(
)
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
d2oo5c_
C:
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
d2oo5a2
A:1-143,A:327-380
2b
d2oo5b2
B:1-143,B:327-380
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
d2oo5a1
A:144-326
3b
d2oo5b1
B:144-326
[
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CATH Domains
(3, 5)
Info
all CATH domains
1a: CATH_2oo5A01 (A:2-143,A:327-370)
1b: CATH_2oo5B01 (B:2-143,B:327-370)
2a: CATH_2oo5A02 (A:144-326)
2b: CATH_2oo5B02 (B:144-326)
3a: CATH_2oo5C00 (C:30-203)
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(
)
(
)
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
2oo5A01
A:2-143,A:327-370
1b
2oo5B01
B:2-143,B:327-370
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Rhodospirillum rubrum. Organism_taxid: 1085.
(11)
2a
2oo5A02
A:144-326
2b
2oo5B02
B:144-326
Homologous Superfamily
:
TPP-binding domain
(120)
Rhodospirillum rubrum. Organism_taxid: 1085.
(13)
3a
2oo5C00
C:30-203
[
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Pfam Domains
(3, 5)
Info
all PFAM domains
1a: PFAM_PNTB_2oo5C01 (C:30-202)
2a: PFAM_AlaDh_PNT_N_2oo5B01 (B:4-144)
2b: PFAM_AlaDh_PNT_N_2oo5B02 (B:4-144)
3a: PFAM_AlaDh_PNT_C_2oo5B03 (B:153-319)
3b: PFAM_AlaDh_PNT_C_2oo5B04 (B:153-319)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
PNTB
(11)
Rhodospirillum rubrum
(9)
1a
PNTB-2oo5C01
C:30-202
Clan
:
Form_Glyc_dh
(56)
Family
:
AlaDh_PNT_N
(24)
Rhodospirillum rubrum
(9)
2a
AlaDh_PNT_N-2oo5B01
B:4-144
2b
AlaDh_PNT_N-2oo5B02
B:4-144
Clan
:
NADP_Rossmann
(1239)
Family
:
AlaDh_PNT_C
(25)
Rhodospirillum rubrum
(9)
3a
AlaDh_PNT_C-2oo5B03
B:153-319
3b
AlaDh_PNT_C-2oo5B04
B:153-319
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