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1ZEM
Asym. Unit
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
(2, 13)
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
5
Ligand/Ion
MAGNESIUM ION
2
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
AC3
SOFTWARE
HOH E:6266 , HOH E:6272 , HOH E:6285 , HOH G:8267 , HOH G:8269 , HOH G:8274
BINDING SITE FOR RESIDUE MG E 3266
04
AC4
SOFTWARE
HOH F:7264 , HOH F:7265 , HOH F:7276 , HOH H:9266 , HOH H:9275 , HOH H:9277
BINDING SITE FOR RESIDUE MG F 3267
05
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
06
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
07
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
08
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
09
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
10
BC1
SOFTWARE
GLY E:14 , GLY E:16 , GLY E:17 , ASN E:18 , ILE E:19 , ASP E:38 , MET E:39 , CYS E:63 , ASP E:64 , VAL E:65 , ASN E:91 , ALA E:92 , GLY E:93 , THR E:142 , ALA E:143 , SER E:144 , TYR E:157 , LYS E:161 , PRO E:187 , GLY E:188 , MET E:190 , MET E:195 , HOH E:6291 , HOH E:6376 , HOH E:6442
BINDING SITE FOR RESIDUE NAD E 6263
11
BC2
SOFTWARE
GLY F:14 , GLY F:16 , GLY F:17 , ASN F:18 , ILE F:19 , ASP F:38 , MET F:39 , CYS F:63 , ASP F:64 , VAL F:65 , ASN F:91 , ALA F:92 , GLY F:93 , THR F:142 , ALA F:143 , SER F:144 , TYR F:157 , LYS F:161 , PRO F:187 , GLY F:188 , MET F:190 , HOH F:7269 , HOH F:7365 , HOH F:7482
BINDING SITE FOR RESIDUE NAD F 7263
12
BC3
SOFTWARE
GLY G:14 , GLY G:16 , GLY G:17 , ASN G:18 , ILE G:19 , ASP G:38 , MET G:39 , CYS G:63 , ASP G:64 , VAL G:65 , ASN G:91 , ALA G:92 , GLY G:93 , THR G:142 , ALA G:143 , SER G:144 , TYR G:157 , LYS G:161 , PRO G:187 , GLY G:188 , MET G:190 , HOH G:8296 , HOH G:8379 , HOH G:8388 , HOH G:8451
BINDING SITE FOR RESIDUE NAD G 8263
13
BC4
SOFTWARE
GLY H:14 , GLY H:17 , ASN H:18 , ILE H:19 , ASP H:38 , MET H:39 , CYS H:63 , ASP H:64 , VAL H:65 , ASN H:91 , ALA H:92 , GLY H:93 , THR H:142 , ALA H:143 , SER H:144 , TYR H:157 , LYS H:161 , PRO H:187 , GLY H:188 , MET H:190 , HOH H:9267 , HOH H:9350 , HOH H:9352 , HOH H:9405 , HOH H:9443 , HOH H:9466
BINDING SITE FOR RESIDUE NAD H 9263
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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[
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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
(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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(
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Superfamilies
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)
(
)
Families
(
)
(
)
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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