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1KOL
Asym. Unit
Info
Asym.Unit (146 KB)
Biol.Unit 1 (277 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FORMALDEHYDE DEHYDROGENASE
Authors
:
N. Tanaka, Y. Kusakabe, K. Ito, T. Yoshimoto, K. T. Nakamura
Date
:
21 Dec 01 (Deposition) - 11 Dec 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Tanaka, Y. Kusakabe, K. Ito, T. Yoshimoto, K. T. Nakamura
Crystal Structure Of Formaldehyde Dehydrogenase From Pseudomonas Putida: The Structural Origin Of The Tightly Bound Cofactor In Nicotinoprotein Dehydrogenases
J. Mol. Biol. V. 324 519 2002
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
SO4
2
Ligand/Ion
SULFATE ION
3
ZN
4
Ligand/Ion
ZINC 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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:46 , HIS A:67 , ASP A:169 , NAD A:1403 , HOH A:1404
BINDING SITE FOR RESIDUE ZN A 1001
2
AC2
SOFTWARE
CYS A:97 , CYS A:100 , CYS A:103 , CYS A:111
BINDING SITE FOR RESIDUE ZN A 1002
3
AC3
SOFTWARE
CYS B:46 , HIS B:67 , ASP B:169 , NAD B:2403 , HOH B:2404
BINDING SITE FOR RESIDUE ZN B 1003
4
AC4
SOFTWARE
CYS B:97 , CYS B:100 , CYS B:103 , CYS B:111
BINDING SITE FOR RESIDUE ZN B 1004
5
AC5
SOFTWARE
PRO A:241 , LEU A:242 , HIS A:269 , HOH A:1548 , HOH A:1618 , HOH A:1634 , HOH A:1735 , HOH A:1836
BINDING SITE FOR RESIDUE SO4 A 1003
6
AC6
SOFTWARE
PRO B:241 , LEU B:242 , HIS B:269 , HOH B:2656 , HOH B:2667 , HOH B:2718 , HOH B:2846
BINDING SITE FOR RESIDUE SO4 B 1002
7
AC7
SOFTWARE
GLY A:47 , SER A:48 , GLN A:50 , HIS A:51 , PHE A:93 , ASP A:169 , THR A:173 , GLY A:193 , GLY A:195 , PRO A:196 , VAL A:197 , GLY A:216 , ASP A:217 , LEU A:218 , ARG A:222 , ALA A:261 , VAL A:262 , ALA A:266 , ARG A:267 , HIS A:269 , VAL A:282 , PRO A:299 , LEU A:301 , TRP A:327 , GLY A:336 , GLN A:337 , THR A:338 , PHE A:379 , ZN A:1001 , HOH A:1409 , HOH A:1415 , HOH A:1426 , HOH A:1450 , HOH A:1467 , HOH A:1579
BINDING SITE FOR RESIDUE NAD A 1403
8
AC8
SOFTWARE
GLY B:47 , SER B:48 , GLN B:50 , HIS B:51 , PHE B:93 , ASP B:169 , THR B:173 , GLY B:193 , GLY B:195 , PRO B:196 , VAL B:197 , GLY B:216 , ASP B:217 , LEU B:218 , ARG B:222 , LEU B:236 , ALA B:261 , VAL B:262 , ALA B:266 , ARG B:267 , HIS B:269 , VAL B:282 , PRO B:299 , LEU B:301 , TRP B:327 , GLY B:336 , GLN B:337 , THR B:338 , PHE B:379 , ZN B:1003 , HOH B:2404 , HOH B:2422 , HOH B:2425 , HOH B:2427 , HOH B:2482 , HOH B:2490 , HOH B:2503 , HOH B:2602 , HOH B:2670 , HOH B:2691
BINDING SITE FOR RESIDUE NAD B 2403
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ADH_ZINC (A:66-80,B:66-80)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_ZINC
PS00059
Zinc-containing alcohol dehydrogenases signature.
FADH_PSEPU
67-81
2
A:66-80
B:66-80
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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_d1kola1 (A:2-160,A:356-397)
1b: SCOP_d1kolb1 (B:2-160,B:356-397)
2a: SCOP_d1kola2 (A:161-355)
2b: SCOP_d1kolb2 (B:161-355)
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)
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)
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)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
GroES-like
(132)
Superfamily
:
GroES-like
(130)
Family
:
Alcohol dehydrogenase-like, N-terminal domain
(114)
Protein domain
:
Formaldehyde dehydrogenase
(1)
Pseudomonas putida [TaxId: 303]
(1)
1a
d1kola1
A:2-160,A:356-397
1b
d1kolb1
B:2-160,B:356-397
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
:
Alcohol dehydrogenase-like, C-terminal domain
(115)
Protein domain
:
Formaldehyde dehydrogenase
(1)
Pseudomonas putida [TaxId: 303]
(1)
2a
d1kola2
A:161-355
2b
d1kolb2
B:161-355
[
close SCOP info
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1kolA02 (A:171-337)
1b: CATH_1kolB02 (B:171-337)
2a: CATH_1kolA01 (A:2-170,A:338-397)
2b: CATH_1kolB01 (B:2-170,B:338-397)
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Homologous Superfamilies
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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)
Pseudomonas putida. Organism_taxid: 303.
(1)
1a
1kolA02
A:171-337
1b
1kolB02
B:171-337
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Quinone Oxidoreductase; Chain A, domain 1
(131)
Homologous Superfamily
:
Medium-chain alcohol dehydrogenases, catalytic domain
(131)
Pseudomonas putida. Organism_taxid: 303.
(1)
2a
1kolA01
A:2-170,A:338-397
2b
1kolB01
B:2-170,B:338-397
[
close CATH info
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_ADH_N_1kolB01 (B:33-151)
1b: PFAM_ADH_N_1kolB02 (B:33-151)
2a: PFAM_AlaDh_PNT_C_1kolB03 (B:173-246)
2b: PFAM_AlaDh_PNT_C_1kolB04 (B:173-246)
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Clans
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)
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)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
GroES
(70)
Family
:
ADH_N
(62)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(1)
1a
ADH_N-1kolB01
B:33-151
1b
ADH_N-1kolB02
B:33-151
Clan
:
NADP_Rossmann
(1239)
Family
:
AlaDh_PNT_C
(25)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(1)
2a
AlaDh_PNT_C-1kolB03
B:173-246
2b
AlaDh_PNT_C-1kolB04
B:173-246
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Asymmetric Unit 1
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