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4LK3
Asym. Unit
Info
Asym.Unit (573 KB)
Biol.Unit 1 (557 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN UDP-XYLOSE SYNTHASE R236A SUBSTITUTION
Authors
:
R. M. Walsh Jr. , S. J. Polizzi, Z. A. Wood
Date
:
05 Jul 13 (Deposition) - 07 Aug 13 (Release) - 03 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.64
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Short-Chain Dehydrogenase/Reductase, Decarboxylase, Lyase, Membrane, Rossmann Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. M. Walsh, S. J. Polizzi, R. Kadirvelraj, W. W. Howard, Z. A. Wood
Man O' War Mutation In Udp-Alpha-D-Xylose Synthase Favors The Abortive Catalytic Cycle And Uncovers A Latent Potentia For Hexamer Formation.
Biochemistry V. 54 807 2015
[
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Hetero Components
(5, 27)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
1e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2a: PYROPHOSPHATE 2- (POPa)
2b: PYROPHOSPHATE 2- (POPb)
2c: PYROPHOSPHATE 2- (POPc)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
4a: URIDINE-5'-DIPHOSPHATE (UDPa)
4b: URIDINE-5'-DIPHOSPHATE (UDPb)
4c: URIDINE-5'-DIPHOSPHATE (UDPc)
5a: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAa)
5b: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAb)
5c: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAc)
5d: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAd)
5e: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAe)
5f: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
6
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
POP
3
Ligand/Ion
PYROPHOSPHATE 2-
3
SO4
9
Ligand/Ion
SULFATE ION
4
UDP
3
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
5
UGA
6
Ligand/Ion
URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID
[
close Hetero Component info
]
Sites
(27, 27)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:95 , ALA A:97 , GLY A:98 , PHE A:99 , VAL A:100 , ASP A:119 , ASN A:120 , PHE A:122 , THR A:123 , GLY A:124 , HIS A:143 , ASP A:144 , VAL A:145 , LEU A:159 , ALA A:160 , SER A:161 , ALA A:163 , THR A:178 , ALA A:200 , SER A:201 , THR A:202 , LYS A:235 , ILE A:258 , PHE A:259 , THR A:261 , HIS A:267
BINDING SITE FOR RESIDUE NAD A 501
02
AC2
SOFTWARE
ARG A:272 , VAL A:273 , ASN A:276 , PHE A:277 , THR A:288 , VAL A:289 , TYR A:290 , GLN A:295 , ARG A:297 , ILE A:331
BINDING SITE FOR RESIDUE UDP A 502
03
AC3
SOFTWARE
PRO A:148 , LEU A:149 , TYR A:150 , ASN A:185 , GLY A:188 , LEU A:189 , LYS A:191 , ARG A:192 , TYR A:245 , GLN A:248 , GLU A:249 , ASN B:171 , ILE B:173 , LYS B:174 , LYS B:177
BINDING SITE FOR RESIDUE UGA A 503
04
AC4
SOFTWARE
ARG A:125 , HIS A:267 , MET A:268 , ASN A:269
BINDING SITE FOR RESIDUE SO4 A 504
05
AC5
SOFTWARE
ARG A:125 , LYS A:126 , ARG A:127 , ARG F:125 , LYS F:126 , ARG F:127
BINDING SITE FOR RESIDUE SO4 A 505
06
AC6
SOFTWARE
GLY B:95 , ALA B:97 , GLY B:98 , PHE B:99 , VAL B:100 , ASP B:119 , ASN B:120 , PHE B:121 , PHE B:122 , THR B:123 , GLY B:124 , HIS B:143 , ASP B:144 , VAL B:145 , LEU B:159 , ALA B:160 , SER B:161 , PRO B:162 , ALA B:163 , THR B:178 , ALA B:200 , SER B:201 , THR B:202 , LYS B:235 , ILE B:258 , PHE B:259 , THR B:261 , HIS B:267 , ARG B:272 , HOH B:615
BINDING SITE FOR RESIDUE NAD B 501
07
AC7
SOFTWARE
GLY B:271 , ARG B:272 , VAL B:273 , ASN B:276 , PHE B:277 , THR B:288 , TYR B:290 , GLN B:295 , ARG B:297 , ILE B:331 , HOH B:613
BINDING SITE FOR RESIDUE UDP B 502
08
AC8
SOFTWARE
LYS A:177 , PRO B:148 , LEU B:149 , TYR B:150 , LEU B:184 , ASN B:185 , GLY B:188 , LEU B:189 , LYS B:191 , ARG B:192 , TYR B:245 , GLN B:248 , GLU B:249
BINDING SITE FOR RESIDUE UGA B 503
09
AC9
SOFTWARE
ARG B:125 , HIS B:267 , MET B:268 , ASN B:269
BINDING SITE FOR RESIDUE SO4 B 504
10
BC1
SOFTWARE
ARG B:125 , LYS B:126 , ARG B:127 , ARG C:125 , LYS C:126 , ARG C:127
BINDING SITE FOR RESIDUE SO4 B 505
11
BC2
SOFTWARE
GLY C:95 , ALA C:97 , GLY C:98 , PHE C:99 , VAL C:100 , ASP C:119 , ASN C:120 , PHE C:122 , THR C:123 , GLY C:124 , HIS C:143 , ASP C:144 , VAL C:145 , LEU C:159 , ALA C:160 , SER C:161 , PRO C:162 , THR C:178 , ALA C:200 , SER C:201 , THR C:202 , LYS C:235 , ILE C:258 , THR C:261 , HIS C:267 , ARG C:272 , HOH C:607 , HOH C:614
BINDING SITE FOR RESIDUE NAD C 501
12
BC3
SOFTWARE
PRO C:148 , LEU C:149 , TYR C:150 , LEU C:184 , ASN C:185 , GLY C:188 , LEU C:189 , LYS C:191 , ARG C:192 , TYR C:245 , GLN C:248 , GLU C:249 , LYS D:177
BINDING SITE FOR RESIDUE UGA C 502
13
BC4
SOFTWARE
ARG C:272 , VAL C:273 , ARG C:297
BINDING SITE FOR RESIDUE POP C 503
14
BC5
SOFTWARE
ARG C:125 , HIS C:267 , MET C:268 , ASN C:269
BINDING SITE FOR RESIDUE SO4 C 504
15
BC6
SOFTWARE
GLY D:95 , ALA D:97 , GLY D:98 , PHE D:99 , VAL D:100 , ASP D:119 , ASN D:120 , PHE D:121 , PHE D:122 , THR D:123 , GLY D:124 , HIS D:143 , ASP D:144 , VAL D:145 , LEU D:159 , SER D:161 , ALA D:163 , THR D:178 , ALA D:200 , SER D:201 , THR D:202 , LYS D:235 , ILE D:258 , PHE D:259 , ASN D:260 , THR D:261 , HIS D:267 , ARG D:272
BINDING SITE FOR RESIDUE NAD D 501
16
BC7
SOFTWARE
ASN D:260 , ARG D:272 , VAL D:273 , ASN D:276 , THR D:288 , TYR D:290 , GLN D:295 , ARG D:297 , ILE D:331
BINDING SITE FOR RESIDUE UDP D 502
17
BC8
SOFTWARE
ASN C:171 , LYS C:177 , PRO D:148 , LEU D:149 , TYR D:150 , ASN D:185 , GLY D:188 , LEU D:189 , LYS D:191 , ARG D:192 , TYR D:245 , GLN D:248 , GLU D:249
BINDING SITE FOR RESIDUE UGA D 503
18
BC9
SOFTWARE
ARG D:125 , LYS D:126 , ARG D:127 , ARG E:125 , LYS E:126 , ARG E:127
BINDING SITE FOR RESIDUE SO4 D 504
19
CC1
SOFTWARE
ARG D:125 , HIS D:267 , MET D:268 , ASN D:269
BINDING SITE FOR RESIDUE SO4 D 505
20
CC2
SOFTWARE
GLY E:95 , ALA E:97 , GLY E:98 , PHE E:99 , VAL E:100 , ASP E:119 , ASN E:120 , PHE E:121 , PHE E:122 , THR E:123 , GLY E:124 , HIS E:143 , ASP E:144 , VAL E:145 , LEU E:159 , ALA E:160 , SER E:161 , THR E:178 , ALA E:200 , SER E:201 , THR E:202 , LYS E:235 , ILE E:258 , THR E:261 , HIS E:267 , ARG E:272
BINDING SITE FOR RESIDUE NAD E 501
21
CC3
SOFTWARE
ARG E:297
BINDING SITE FOR RESIDUE POP E 502
22
CC4
SOFTWARE
PRO E:148 , LEU E:149 , TYR E:150 , ASN E:185 , GLY E:188 , LEU E:189 , LYS E:191 , ARG E:192 , TYR E:245 , GLN E:248 , GLU E:249 , HOH E:602 , LYS F:177
BINDING SITE FOR RESIDUE UGA E 503
23
CC5
SOFTWARE
ARG E:125 , HIS E:267 , MET E:268 , ASN E:269
BINDING SITE FOR RESIDUE SO4 E 504
24
CC6
SOFTWARE
GLY F:95 , ALA F:97 , GLY F:98 , PHE F:99 , VAL F:100 , ASP F:119 , ASN F:120 , PHE F:121 , PHE F:122 , THR F:123 , GLY F:124 , HIS F:143 , ASP F:144 , VAL F:145 , LEU F:159 , ALA F:160 , SER F:161 , THR F:178 , SER F:201 , THR F:202 , LYS F:235 , ILE F:258 , PHE F:259 , THR F:261 , HIS F:267 , ARG F:272
BINDING SITE FOR RESIDUE NAD F 501
25
CC7
SOFTWARE
LYS E:174 , LYS E:177 , PRO F:148 , LEU F:149 , TYR F:150 , ASN F:185 , GLY F:188 , LEU F:189 , LYS F:191 , ARG F:192 , TYR F:245 , GLN F:248 , GLU F:249
BINDING SITE FOR RESIDUE UGA F 502
26
CC8
SOFTWARE
ASN F:260 , ARG F:272 , VAL F:273 , ARG F:297 , PHE F:299
BINDING SITE FOR RESIDUE POP F 503
27
CC9
SOFTWARE
ARG F:125 , HIS F:267 , MET F:268 , ASN F:269
BINDING SITE FOR RESIDUE SO4 F 504
[
close Site info
]
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
(0, 0)
Info
All PROSITE Patterns/Profiles
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d4lk3a_ (A:)
1b: SCOP_d4lk3b_ (B:)
1c: SCOP_d4lk3c_ (C:)
1d: SCOP_d4lk3d_ (D:)
1e: SCOP_d4lk3e_ (E:)
1f: SCOP_d4lk3f_ (F:)
View:
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Classes
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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)
Human (Homo sapiens) [TaxId: 9606]
(32)
1a
d4lk3a_
A:
1b
d4lk3b_
B:
1c
d4lk3c_
C:
1d
d4lk3d_
D:
1e
d4lk3e_
E:
1f
d4lk3f_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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