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1ZEM
Biol. Unit 3
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
(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 only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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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.
(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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)
(
)
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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