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1NM5
Asym. Unit
Info
Asym.Unit (144 KB)
Biol.Unit 1 (138 KB)
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(1)
Title
:
R. RUBRUM TRANSHYDROGENASE (DI.Q132N)2(DIII)1 ASYMMETRIC COMPLEX
Authors
:
G. I. Van Boxel, P. G. Quirk, N. P. Cotton, S. A. White, J. B. Jackson
Date
:
09 Jan 03 (Deposition) - 13 Jan 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Asymmetric Complex, Rossman Domain, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. I. Van Boxel, P. G. Quirk, N. P. Cotton, S. A. White, J. B. Jackson
Glutamine 132 In The Nad(H)-Binding Component Of Proton-Translocating Transhydrogenase Tethers The Nucleotides Before Hydride Transfer.
Biochemistry V. 42 1217 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
NAP
1
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:127 , ILE A:128 , ASN A:132 , ASP A:135 , SER A:138 , GLY A:179 , VAL A:182 , ASP A:202 , VAL A:203 , ARG A:204 , ALA A:236 , GLN A:247 , THR A:264 , ALA A:265 , LEU A:266 , LEU A:275 , HOH A:401 , HOH A:410
BINDING SITE FOR RESIDUE NAD A 400
2
AC2
SOFTWARE
GLY B:181 , VAL B:182 , ASP B:202 , ARG B:204 , THR B:264 , LEU B:275
BINDING SITE FOR RESIDUE NAD B 500
3
AC3
SOFTWARE
ASN B:132 , GLY C:54 , TYR C:55 , GLY C:56 , ALA C:60 , VAL C:87 , ALA C:88 , 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 , SER C:169 , GLY C:170 , TYR C:171 , ASP C:190 , ALA C:191
BINDING SITE FOR RESIDUE NAP C 300
4
AC4
SOFTWARE
ARG B:15 , GLN B:75 , HIS B:99 , ASN B:322 , PRO B:324
BINDING SITE FOR RESIDUE GOL B 501
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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...)
;
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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
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, 5)
Info
All SCOP Domains
1a: SCOP_d1nm5c_ (C:)
2a: SCOP_d1nm5a2 (A:1-143,A:327-374)
2b: SCOP_d1nm5b2 (B:1-143,B:327-378)
3a: SCOP_d1nm5a1 (A:144-326)
3b: SCOP_d1nm5b1 (B:144-326)
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)
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)
(
)
Families
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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
d1nm5c_
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
d1nm5a2
A:1-143,A:327-374
2b
d1nm5b2
B:1-143,B:327-378
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
d1nm5a1
A:144-326
3b
d1nm5b1
B:144-326
[
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CATH Domains
(3, 5)
Info
all CATH domains
1a: CATH_1nm5A02 (A:2-143,A:327-372)
1b: CATH_1nm5B02 (B:2-143,B:327-372)
2a: CATH_1nm5A01 (A:144-326)
2b: CATH_1nm5B01 (B:144-326)
3a: CATH_1nm5C00 (C:30-203)
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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
:
[code=3.40.50.1770, no name defined]
(22)
Rhodospirillum rubrum. Organism_taxid: 1085.
(11)
1a
1nm5A02
A:2-143,A:327-372
1b
1nm5B02
B:2-143,B:327-372
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Rhodospirillum rubrum. Organism_taxid: 1085.
(11)
2a
1nm5A01
A:144-326
2b
1nm5B01
B:144-326
Homologous Superfamily
:
TPP-binding domain
(120)
Rhodospirillum rubrum. Organism_taxid: 1085.
(13)
3a
1nm5C00
C:30-203
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Pfam Domains
(3, 5)
Info
all PFAM domains
1a: PFAM_PNTB_1nm5C01 (C:30-202)
2a: PFAM_AlaDh_PNT_N_1nm5B01 (B:4-144)
2b: PFAM_AlaDh_PNT_N_1nm5B02 (B:4-144)
3a: PFAM_AlaDh_PNT_C_1nm5B03 (B:153-319)
3b: PFAM_AlaDh_PNT_C_1nm5B04 (B:153-319)
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)
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
PNTB
(11)
Rhodospirillum rubrum
(9)
1a
PNTB-1nm5C01
C:30-202
Clan
:
Form_Glyc_dh
(56)
Family
:
AlaDh_PNT_N
(24)
Rhodospirillum rubrum
(9)
2a
AlaDh_PNT_N-1nm5B01
B:4-144
2b
AlaDh_PNT_N-1nm5B02
B:4-144
Clan
:
NADP_Rossmann
(1239)
Family
:
AlaDh_PNT_C
(25)
Rhodospirillum rubrum
(9)
3a
AlaDh_PNT_C-1nm5B03
B:153-319
3b
AlaDh_PNT_C-1nm5B04
B:153-319
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Asymmetric Unit 1
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Asym.Unit (144 KB)
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