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3WDP
Asym. Unit
Info
Asym.Unit (350 KB)
Biol.Unit 1 (177 KB)
Biol.Unit 2 (173 KB)
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(1)
Title
:
STRUCTURAL ANALYSIS OF A BETA-GLUCOSIDASE MUTANT DERIVED FROM A HYPERTHERMOPHILIC TETRAMERIC STRUCTURE
Authors
:
M. Nakabayashi, M. Kataoka, K. Ishikawa
Date
:
19 Jun 13 (Deposition) - 12 Mar 14 (Release) - 12 Mar 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : P,Q,R,S
Biol. Unit 1: P,Q (1x)
Biol. Unit 2: R,S (1x)
Keywords
:
Tim Barrel, Hydrolase, Sugar Binding, Hydrolysis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Nakabayashi, M. Kataoka, Y. Mishima, Y. Maeno, K. Ishikawa
Structural Analysis Of Beta-Glucosidase Mutants Derived Fro A Hyperthermophilic Tetrameric Structure
Acta Crystallogr. , Sect. D V. 70 877 2014
[
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Hetero Components
(2, 23)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
2h: PHOSPHATE ION (PO4h)
2i: PHOSPHATE ION (PO4i)
2j: PHOSPHATE ION (PO4j)
2k: PHOSPHATE ION (PO4k)
2l: PHOSPHATE ION (PO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
11
Ligand/Ion
GLYCEROL
2
PO4
12
Ligand/Ion
PHOSPHATE ION
[
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Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN P:17 , HIS P:150 , ASN P:206 , GLU P:207 , GLU P:372 , TRP P:410 , GLU P:417 , TRP P:418 , GOL P:503 , GOL P:504
BINDING SITE FOR RESIDUE GOL P 501
02
AC2
SOFTWARE
THR P:143 , MET P:201 , HOH P:928 , HOH P:978
BINDING SITE FOR RESIDUE GOL P 502
03
AC3
SOFTWARE
PHE P:344 , GLU P:417 , GOL P:501 , GOL P:504 , HOH P:622 , HOH P:903
BINDING SITE FOR RESIDUE GOL P 503
04
AC4
SOFTWARE
GLU P:207 , ALA P:264 , TYR P:307 , GOL P:501 , GOL P:503 , HOH P:714
BINDING SITE FOR RESIDUE GOL P 504
05
AC5
SOFTWARE
PHE P:422 , ARG P:425 , HOH P:803 , HOH P:936 , HOH P:1013 , PHE Q:468
BINDING SITE FOR RESIDUE PO4 P 505
06
AC6
SOFTWARE
PHE P:91 , LYS P:179 , GLU P:183 , LYS P:186 , HOH P:687 , HOH P:1021
BINDING SITE FOR RESIDUE PO4 P 506
07
AC7
SOFTWARE
ASN P:213 , LYS P:237 , HOH P:621 , HOH P:676 , HOH P:844 , HOH P:845
BINDING SITE FOR RESIDUE PO4 P 507
08
AC8
SOFTWARE
ILE P:106 , LYS P:298 , HOH P:619 , HOH P:734 , HOH P:736
BINDING SITE FOR RESIDUE PO4 P 508
09
AC9
SOFTWARE
GLN Q:17 , HIS Q:150 , ASN Q:206 , GLU Q:207 , GLU Q:372 , TRP Q:410 , GLU Q:417 , TRP Q:418 , GOL Q:502 , GOL Q:503
BINDING SITE FOR RESIDUE GOL Q 501
10
BC1
SOFTWARE
PHE Q:344 , GLU Q:417 , GOL Q:501 , GOL Q:503 , HOH Q:626
BINDING SITE FOR RESIDUE GOL Q 502
11
BC2
SOFTWARE
GLU Q:207 , VAL Q:210 , ALA Q:264 , TYR Q:307 , GOL Q:501 , GOL Q:502 , HOH Q:712
BINDING SITE FOR RESIDUE GOL Q 503
12
BC3
SOFTWARE
ASP Q:37 , GLU Q:39 , ILE Q:161 , LYS Q:165 , HOH Q:786
BINDING SITE FOR RESIDUE PO4 Q 504
13
BC4
SOFTWARE
PHE P:468 , PHE Q:422 , ARG Q:425 , HOH Q:797 , HOH Q:798 , HOH Q:1014
BINDING SITE FOR RESIDUE PO4 Q 505
14
BC5
SOFTWARE
PHE Q:91 , LYS Q:94 , LYS Q:179 , GLU Q:183 , LYS Q:186 , HOH Q:706 , HOH Q:980
BINDING SITE FOR RESIDUE PO4 Q 506
15
BC6
SOFTWARE
ASN Q:213 , LYS Q:237 , HOH Q:612 , HOH Q:676 , HOH Q:869 , HOH Q:892
BINDING SITE FOR RESIDUE PO4 Q 507
16
BC7
SOFTWARE
GLN R:17 , HIS R:150 , ASN R:206 , GLU R:207 , GLU R:372 , TRP R:410 , GLU R:417 , TRP R:418 , GOL R:503
BINDING SITE FOR RESIDUE GOL R 501
17
BC8
SOFTWARE
GLU Q:128 , ARG Q:131 , ARG R:131 , LYS R:132 , SER R:135 , HOH R:665 , HOH R:874
BINDING SITE FOR RESIDUE GOL R 502
18
BC9
SOFTWARE
GLU R:207 , VAL R:210 , TYR R:307 , GOL R:501 , HOH R:869
BINDING SITE FOR RESIDUE GOL R 503
19
CC1
SOFTWARE
PHE R:91 , LYS R:94 , LYS R:179 , VAL R:182 , GLU R:183 , LYS R:186 , HOH R:685 , HOH R:790
BINDING SITE FOR RESIDUE PO4 R 504
20
CC2
SOFTWARE
TYR R:212 , ASN R:213 , GLU R:234 , LYS R:237 , HOH R:656 , HOH R:892
BINDING SITE FOR RESIDUE PO4 R 505
21
CC3
SOFTWARE
ASP R:269 , PRO R:270 , ARG R:309 , HOH R:831
BINDING SITE FOR RESIDUE PO4 R 506
22
CC4
SOFTWARE
GLN S:17 , HIS S:150 , ASN S:206 , GLU S:207 , GLU S:372 , TRP S:410 , GLU S:417 , TRP S:418
BINDING SITE FOR RESIDUE GOL S 501
23
CC5
SOFTWARE
PHE S:91 , LYS S:179 , VAL S:182 , GLU S:183 , LYS S:186 , HOH S:710 , HOH S:829
BINDING SITE FOR RESIDUE PO4 S 502
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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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:
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3wdpp_ (P:)
1b: SCOP_d3wdpq_ (Q:)
1c: SCOP_d3wdpr_ (R:)
1d: SCOP_d3wdps_ (S:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
Family 1 of glycosyl hydrolase
(102)
Protein domain
:
automated matches
(36)
Pyrococcus furiosus [TaxId: 2261]
(2)
1a
d3wdpp_
P:
1b
d3wdpq_
Q:
1c
d3wdpr_
R:
1d
d3wdps_
S:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Nucleic
Backbone
Sidechain
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain P
Chain Q
Chain R
Chain S
Asymmetric Unit 1
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Example Commands
Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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Show PDB file:
Asym.Unit (350 KB)
Header - Asym.Unit
Biol.Unit 1 (177 KB)
Header - Biol.Unit 1
Biol.Unit 2 (173 KB)
Header - Biol.Unit 2
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