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1ZEM
Biol. Unit 1
Info
Asym.Unit (358 KB)
Biol.Unit 1 (179 KB)
Biol.Unit 2 (178 KB)
Biol.Unit 3 (351 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NAD+-BOUND XYLITOL DEHYDROGENASE
Authors
:
A. H. Ehrensberger, R. A. Elling, D. K. Wilson
Date
:
19 Apr 05 (Deposition) - 28 Mar 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: A,B,C,D,E,F,G,H (1x)
Keywords
:
Rossmann Fold, Dinucleotide-Binding Domain, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. H. Ehrensberger, R. A. Elling, D. K. Wilson
Structure-Guided Engineering Of Xylitol Dehydrogenase Cosubstrate Specificity.
Structure V. 14 567 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
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)
2f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
2h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
7: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH B:3267 , HOH B:3277 , HOH D:5264 , HOH D:5271 , HOH D:5273 , HOH D:5288
BINDING SITE FOR RESIDUE MG D 3264
2
AC2
SOFTWARE
HOH A:2270 , HOH A:2275 , HOH A:2338 , HOH C:4265 , HOH C:4279 , HOH C:4446
BINDING SITE FOR RESIDUE MG C 3265
3
AC5
SOFTWARE
HOH C:4362 , HOH C:4376 , HOH C:4392 , HOH C:4428 , HOH C:4429 , HOH C:4430
BINDING SITE FOR RESIDUE MG C 3268
4
AC6
SOFTWARE
GLY A:14 , GLY A:16 , GLY A:17 , ASN A:18 , ILE A:19 , ASP A:38 , MET A:39 , CYS A:63 , ASP A:64 , VAL A:65 , ASN A:91 , ALA A:92 , GLY A:93 , ILE A:115 , THR A:142 , ALA A:143 , SER A:144 , TYR A:157 , LYS A:161 , PRO A:187 , GLY A:188 , MET A:190 , HOH A:2268 , HOH A:2385 , HOH A:2422
BINDING SITE FOR RESIDUE NAD A 2263
5
AC7
SOFTWARE
GLY B:14 , GLY B:16 , GLY B:17 , ASN B:18 , ILE B:19 , ASP B:38 , MET B:39 , CYS B:63 , ASP B:64 , VAL B:65 , ASN B:91 , ALA B:92 , GLY B:93 , ILE B:115 , THR B:142 , ALA B:143 , SER B:144 , TYR B:157 , LYS B:161 , PRO B:187 , GLY B:188 , MET B:190 , HOH B:3297 , HOH B:3343 , HOH B:3398 , HOH B:3418 , HOH B:3420 , HOH B:3431 , HOH B:3460
BINDING SITE FOR RESIDUE NAD B 3263
6
AC8
SOFTWARE
GLY C:14 , GLY C:16 , GLY C:17 , ASN C:18 , ILE C:19 , ASP C:38 , MET C:39 , CYS C:63 , ASP C:64 , VAL C:65 , ASN C:91 , ALA C:92 , GLY C:93 , ILE C:115 , THR C:142 , ALA C:143 , SER C:144 , TYR C:157 , LYS C:161 , PRO C:187 , MET C:190 , MET C:195 , HOH C:4267 , HOH C:4295 , HOH C:4321 , HOH C:4360 , HOH C:4366 , HOH C:4384 , HOH C:4387 , HOH C:4431 , HOH C:4432 , HOH C:4435 , HOH C:4507
BINDING SITE FOR RESIDUE NAD C 4263
7
AC9
SOFTWARE
GLY D:14 , GLY D:16 , GLY D:17 , ASN D:18 , ILE D:19 , ASP D:38 , MET D:39 , CYS D:63 , ASP D:64 , VAL D:65 , ASN D:91 , ALA D:92 , GLY D:93 , ILE D:115 , THR D:142 , ALA D:143 , SER D:144 , TYR D:157 , LYS D:161 , PRO D:187 , GLY D:188 , MET D:190 , MET D:195 , HOH D:5265 , HOH D:5392 , HOH D:5411 , HOH D:5451
BINDING SITE FOR RESIDUE NAD D 5263
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1zemb_ (B:)
1b: SCOP_d1zemh_ (H:)
1c: SCOP_d1zemc_ (C:)
1d: SCOP_d1zemd_ (D:)
1e: SCOP_d1zeme_ (E:)
1f: SCOP_d1zemf_ (F:)
1g: SCOP_d1zemg_ (G:)
2a: SCOP_d1zema1 (A:3-262)
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Gluconobacter oxydans [TaxId: 442]
(2)
1a
d1zemb_
B:
1b
d1zemh_
H:
1c
d1zemc_
C:
1d
d1zemd_
D:
1e
d1zeme_
E:
1f
d1zemf_
F:
1g
d1zemg_
G:
Family
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
Xylitol dehydrogenase
(1)
Gluconobacter oxydans [TaxId: 442]
(1)
2a
d1zema1
A:3-262
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1zemA00 (A:3-262)
1b: CATH_1zemB00 (B:3-262)
1c: CATH_1zemC00 (C:3-262)
1d: CATH_1zemD00 (D:3-262)
1e: CATH_1zemE00 (E:3-262)
1f: CATH_1zemF00 (F:3-262)
1g: CATH_1zemG00 (G:3-262)
1h: CATH_1zemH00 (H:3-262)
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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)
Gluconobacter oxydans. Organism_taxid: 442.
(1)
1a
1zemA00
A:3-262
1b
1zemB00
B:3-262
1c
1zemC00
C:3-262
1d
1zemD00
D:3-262
1e
1zemE00
E:3-262
1f
1zemF00
F:3-262
1g
1zemG00
G:3-262
1h
1zemH00
H:3-262
[
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Pfam Domains
(0, 0)
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Chain C
Chain D
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (358 KB)
Header - Asym.Unit
Biol.Unit 1 (179 KB)
Header - Biol.Unit 1
Biol.Unit 2 (178 KB)
Header - Biol.Unit 2
Biol.Unit 3 (351 KB)
Header - Biol.Unit 3
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