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2NAD
Asym. Unit
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Asym.Unit (146 KB)
Biol.Unit 1 (140 KB)
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(1)
Title
:
HIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE
Authors
:
V. S. Lamzin, Z. Dauter, V. O. Popov, E. H. Harutyunyan, K. S. Wilson
Date
:
06 Jul 94 (Deposition) - 26 Jan 95 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase(Aldehyde(D), Nad+(A))
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
V. S. Lamzin, Z. Dauter, V. O. Popov, E. H. Harutyunyan, K. S. Wilson
High Resolution Structures Of Holo And Apo Formate Dehydrogenase.
J. Mol. Biol. V. 236 759 1994
(for further references see the
PDB file header
)
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Hetero Components
(3, 5)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
1b: AZIDE ION (AZIb)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: SULFATE ION (SO4a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AZI
2
Ligand/Ion
AZIDE ION
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:97 , PHE A:98 , GLY A:121 , ILE A:122 , ASN A:146 , ARG A:284 , HIS A:332 , NAD A:394
BINDING SITE FOR RESIDUE AZI A 395
2
AC2
SOFTWARE
HOH A:523 , HIS B:263 , LYS B:286 , CYS B:288 , ASP B:289 , ARG B:290 , HOH B:448 , HOH B:675
BINDING SITE FOR RESIDUE SO4 A 396
3
AC3
SOFTWARE
PRO B:97 , PHE B:98 , ILE B:122 , ASN B:146 , ARG B:284 , HIS B:332 , NAD B:394
BINDING SITE FOR RESIDUE AZI B 395
4
AC4
SOFTWARE
PHE A:98 , ILE A:122 , ASN A:146 , SER A:147 , VAL A:150 , ALA A:198 , GLY A:200 , ARG A:201 , ILE A:202 , ASP A:221 , ARG A:222 , HIS A:223 , ASN A:254 , PRO A:256 , HIS A:258 , GLU A:260 , THR A:261 , THR A:282 , ALA A:283 , ARG A:284 , ASP A:308 , VAL A:309 , HIS A:332 , SER A:334 , GLY A:335 , SER A:380 , TYR A:381 , AZI A:395 , HOH A:409 , HOH A:412 , HOH A:425 , HOH A:453 , HOH A:460 , HOH A:499 , HOH A:578
BINDING SITE FOR RESIDUE NAD A 394
5
AC5
SOFTWARE
PHE B:98 , ILE B:122 , ASN B:146 , SER B:147 , VAL B:150 , ALA B:198 , GLY B:200 , ARG B:201 , ILE B:202 , ASP B:221 , ARG B:222 , HIS B:223 , ASN B:254 , PRO B:256 , HIS B:258 , GLU B:260 , THR B:261 , THR B:282 , ALA B:283 , ARG B:284 , ASP B:308 , HIS B:332 , SER B:334 , GLY B:335 , SER B:380 , TYR B:381 , AZI B:395 , HOH B:397 , HOH B:398 , HOH B:399 , HOH B:400 , HOH B:426 , HOH B:436 , HOH B:495 , HOH B:575
BINDING SITE FOR RESIDUE NAD B 394
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: D_2_HYDROXYACID_DH_1 (A:194-221,B:194-221)
2: D_2_HYDROXYACID_DH_2 (A:244-266,B:244-266)
3: D_2_HYDROXYACID_DH_3 (A:273-289,B:273-289)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
D_2_HYDROXYACID_DH_1
PS00065
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.
FDH_PSESR
195-222
2
A:194-221
B:194-221
2
D_2_HYDROXYACID_DH_2
PS00670
D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
FDH_PSESR
245-267
2
A:244-266
B:244-266
3
D_2_HYDROXYACID_DH_3
PS00671
D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
FDH_PSESR
274-290
2
A:273-289
B:273-289
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 4)
Info
All SCOP Domains
1a: SCOP_d2nada2 (A:1-147,A:336-391)
1b: SCOP_d2nadb2 (B:1-147,B:336-383)
2a: SCOP_d2nada1 (A:148-335)
2b: SCOP_d2nadb1 (B:148-335)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
Formate/glycerate dehydrogenases, substrate-binding domain
(21)
Protein domain
:
Formate dehydrogenase
(2)
Pseudomonas sp., strain 101 [TaxId: 306]
(2)
1a
d2nada2
A:1-147,A:336-391
1b
d2nadb2
B:1-147,B:336-383
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
:
Formate dehydrogenase
(2)
Pseudomonas sp., strain 101 [TaxId: 306]
(2)
2a
d2nada1
A:148-335
2b
d2nadb1
B:148-335
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2nadA02 (A:146-335)
1b: CATH_2nadA01 (A:1-145,A:336-374)
1c: CATH_2nadB01 (B:1-145,B:336-374)
1d: CATH_2nadB02 (B:146-335)
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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)
101 (Pseudomonas sp)
(4)
1a
2nadA02
A:146-335
1b
2nadA01
A:1-145,A:336-374
1c
2nadB01
B:1-145,B:336-374
1d
2nadB02
B:146-335
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_2_Hacid_dh_2nadB01 (B:56-365)
1b: PFAM_2_Hacid_dh_2nadB02 (B:56-365)
2a: PFAM_2_Hacid_dh_C_2nadB03 (B:155-334)
2b: PFAM_2_Hacid_dh_C_2nadB04 (B:155-334)
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Clan
:
Form_Glyc_dh
(56)
Family
:
2-Hacid_dh
(21)
Pseudomonas sp. (strain 101) (Achromobacter parvulus T1)
(2)
1a
2-Hacid_dh-2nadB01
B:56-365
1b
2-Hacid_dh-2nadB02
B:56-365
Clan
:
NADP_Rossmann
(1239)
Family
:
2-Hacid_dh_C
(23)
Pseudomonas sp. (strain 101) (Achromobacter parvulus T1)
(2)
2a
2-Hacid_dh_C-2nadB03
B:155-334
2b
2-Hacid_dh_C-2nadB04
B:155-334
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Asym.Unit (146 KB)
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