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1Y7B
Asym. Unit
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Asym.Unit (421 KB)
Biol.Unit 1 (413 KB)
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(1)
Title
:
BETA-D-XYLOSIDASE, A FAMILY 43 GLYCOSIDE HYDROLASE
Authors
:
A. Teplyakov, E. Fedorov, G. L. Gilliland, S. C. Almo, S. K. Burley, New Research Center For Structural Genomics (Nysgxrc)
Date
:
08 Dec 04 (Deposition) - 25 Jan 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Beta-Propeller, Beta-Sandwich, Structural Genomics, Protein Structure Initative, Psi, New York Sgx Research Center For Structural Genomics, Nysgxrc, Protein Structure Initiative, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Teplyakov, E. Fedorov, G. L. Gilliland, S. C. Almo, New York Structural Genomics Research Consortium (Nysgrc)
Crystal Structure Of Beta-Xylosidase From Clostridium Acetobutylicum
To Be Published
[
close entry info
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Hetero Components
(5, 29)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
2d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
4a: TRIETHYLENE GLYCOL (PGEa)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
GOL
14
Ligand/Ion
GLYCEROL
4
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
5
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:333 , GLY A:362 , ASP A:528 , HOH A:3212 , HOH A:3234
BINDING SITE FOR RESIDUE CA A 3001
02
AC2
SOFTWARE
ASN B:333 , GLY B:362 , ASP B:528 , HOH B:3165 , HOH B:3213
BINDING SITE FOR RESIDUE CA B 3002
03
AC3
SOFTWARE
ASN C:333 , GLY C:362 , ASP C:528 , HOH C:3234 , HOH C:3258
BINDING SITE FOR RESIDUE CA C 3003
04
AC4
SOFTWARE
ASN D:333 , GLY D:362 , ASP D:528 , HOH D:3213 , HOH D:3263
BINDING SITE FOR RESIDUE CA D 3004
05
AC5
SOFTWARE
SER D:311 , VAL D:312 , ASN D:313 , HOH D:3320 , HOH D:3562 , HOH D:3756
BINDING SITE FOR RESIDUE SO4 D 3024
06
AC6
SOFTWARE
SER B:311 , VAL B:312 , ASN B:313 , HOH B:3256 , HOH B:3519 , HOH B:3547 , HOH B:3649 , HOH B:3664
BINDING SITE FOR RESIDUE SO4 B 3025
07
AC7
SOFTWARE
LYS B:326 , THR B:327 , TYR B:328 , HOH B:3204 , HOH B:3217 , HOH B:3278 , HOH B:3302 , HOH B:3342 , HOH B:3446 , HOH B:3730
BINDING SITE FOR RESIDUE SO4 B 3026
08
AC8
SOFTWARE
LYS A:326 , THR A:327 , HOH A:3205 , HOH A:3249 , HOH A:3277 , HOH A:3287 , HOH A:3335
BINDING SITE FOR RESIDUE SO4 A 3027
09
AC9
SOFTWARE
LYS D:326 , THR D:327 , HOH D:3274 , HOH D:3275 , HOH D:3291 , HOH D:3354 , HOH D:3412
BINDING SITE FOR RESIDUE SO4 D 3028
10
BC1
SOFTWARE
ARG A:58 , THR A:59 , SER A:60 , HOH A:3145 , HOH A:3610 , HOH A:3717
BINDING SITE FOR RESIDUE SO4 A 3029
11
BC2
SOFTWARE
ASP A:401 , TYR B:156 , LYS B:173 , ALA B:174 , HOH B:3118 , HOH B:3338 , HOH B:3378 , HOH B:3410 , HOH B:3493
BINDING SITE FOR RESIDUE EPE B 3005
12
BC3
SOFTWARE
TYR A:156 , LYS A:173 , ALA A:174 , HOH A:3132 , HOH A:3346 , HOH A:3512 , HOH A:3551 , HOH A:3615 , ASP B:401 , TRP B:425 , HOH B:3138
BINDING SITE FOR RESIDUE EPE A 3006
13
BC4
SOFTWARE
ASP C:401 , HOH C:3151 , HOH C:3237 , TYR D:156 , LYS D:173 , ALA D:174 , HOH D:3129 , HOH D:3382 , HOH D:3555 , HOH D:3599 , HOH D:3758
BINDING SITE FOR RESIDUE EPE D 3007
14
BC5
SOFTWARE
TYR C:156 , LYS C:173 , ALA C:174 , HOH C:3079 , HOH C:3276 , HOH C:3501 , ASP D:401 , TRP D:425
BINDING SITE FOR RESIDUE EPE C 3008
15
BC6
SOFTWARE
ILE A:194 , GLY A:195 , ASP A:196 , TYR A:199 , TRP A:297 , ASN A:300 , HOH A:3401 , HOH A:3474 , HOH A:3606
BINDING SITE FOR RESIDUE PGE A 3023
16
BC7
SOFTWARE
SER B:60 , LEU B:61 , LEU B:62 , ASP B:63 , ASP B:91 , TYR B:105 , PRO B:119 , HOH B:3106 , HOH B:3140 , HOH B:3314 , HOH B:3604
BINDING SITE FOR RESIDUE GOL B 3009
17
BC8
SOFTWARE
ASP B:15 , PHE B:32 , TRP B:74 , ALA B:75 , ASP B:128 , ARG B:288 , GOL B:3018 , HOH B:3065
BINDING SITE FOR RESIDUE GOL B 3010
18
BC9
SOFTWARE
ASP A:15 , PHE A:32 , TRP A:74 , ALA A:75 , ASP A:128 , ARG A:288 , GOL A:3017 , HOH A:3035
BINDING SITE FOR RESIDUE GOL A 3011
19
CC1
SOFTWARE
SER A:60 , LEU A:61 , LEU A:62 , ASP A:63 , ASP A:91 , PRO A:119 , HOH A:3082 , HOH A:3186 , HOH A:3470 , HOH A:3488
BINDING SITE FOR RESIDUE GOL A 3012
20
CC2
SOFTWARE
SER C:60 , LEU C:61 , ASP C:63 , ASP C:91 , TYR C:105 , PRO C:119 , HOH C:3088 , HOH C:3126 , HOH C:3243
BINDING SITE FOR RESIDUE GOL C 3013
21
CC3
SOFTWARE
ASP C:15 , PHE C:32 , TRP C:74 , ALA C:75 , ASP C:128 , ARG C:288 , HOH C:3030 , HOH C:3583
BINDING SITE FOR RESIDUE GOL C 3014
22
CC4
SOFTWARE
ASP D:15 , PHE D:32 , TRP D:74 , ALA D:75 , ASP D:128 , ARG D:288 , GOL D:3019 , HOH D:3081
BINDING SITE FOR RESIDUE GOL D 3015
23
CC5
SOFTWARE
SER D:60 , LEU D:61 , LEU D:62 , ASP D:63 , ASP D:91 , TYR D:105 , PRO D:119 , HOH D:3093 , HOH D:3170 , HOH D:3234 , HOH D:3331
BINDING SITE FOR RESIDUE GOL D 3016
24
CC6
SOFTWARE
PHE A:155 , TYR A:185 , GLU A:187 , GLY A:206 , THR A:207 , GOL A:3011 , HOH A:3310
BINDING SITE FOR RESIDUE GOL A 3017
25
CC7
SOFTWARE
GLU B:187 , GLY B:206 , THR B:207 , GOL B:3010 , HOH B:3230
BINDING SITE FOR RESIDUE GOL B 3018
26
CC8
SOFTWARE
GLU D:187 , GLY D:206 , THR D:207 , GOL D:3015 , HOH D:3294 , HOH D:3418
BINDING SITE FOR RESIDUE GOL D 3019
27
CC9
SOFTWARE
ILE C:194 , TYR C:199 , ASN C:300
BINDING SITE FOR RESIDUE GOL C 3020
28
DC1
SOFTWARE
PRO B:240 , ARG B:241 , HOH B:3316 , HOH B:3393 , HOH B:3663 , ILE D:183 , PRO D:232 , HOH D:3287
BINDING SITE FOR RESIDUE GOL B 3021
29
DC2
SOFTWARE
PRO A:240 , ARG A:241 , HOH A:3293 , HOH A:3316 , HOH A:3477 , HOH A:3822 , PRO C:232 , HOH C:3351
BINDING SITE FOR RESIDUE GOL A 3022
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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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
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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_d1y7ba2 (A:4-324)
1b: SCOP_d1y7bb2 (B:2-324)
1c: SCOP_d1y7bc2 (C:2-324)
1d: SCOP_d1y7bd2 (D:2-324)
2a: SCOP_d1y7ba1 (A:325-534)
2b: SCOP_d1y7bb1 (B:325-535)
2c: SCOP_d1y7bc1 (C:325-535)
2d: SCOP_d1y7bd1 (D:325-535)
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)
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Folds
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)
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)
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
5-bladed beta-propeller
(42)
Superfamily
:
Arabinanase/levansucrase/invertase
(37)
Family
:
alpha-L-arabinanase-like
(18)
Protein domain
:
Beta-D-xylosidase N-terminal domain
(8)
Clostridium acetobutylicum [TaxId: 1488]
(2)
1a
d1y7ba2
A:4-324
1b
d1y7bb2
B:2-324
1c
d1y7bc2
C:2-324
1d
d1y7bd2
D:2-324
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Beta-D-xylosidase C-terminal domain-like
(8)
Protein domain
:
Beta-D-xylosidase C-terminal domain
(8)
Clostridium acetobutylicum [TaxId: 1488]
(2)
2a
d1y7ba1
A:325-534
2b
d1y7bb1
B:325-535
2c
d1y7bc1
C:325-535
2d
d1y7bd1
D:325-535
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1y7bA01 (A:2-326)
1b: CATH_1y7bB01 (B:2-326)
1c: CATH_1y7bC01 (C:2-326)
1d: CATH_1y7bD01 (D:2-326)
2a: CATH_1y7bA02 (A:327-535)
2b: CATH_1y7bB02 (B:327-535)
2c: CATH_1y7bC02 (C:327-535)
2d: CATH_1y7bD02 (D:327-535)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
5 Propellor
(21)
Topology
:
Tachylectin-2; Chain A
(21)
Homologous Superfamily
:
Glycosyl hydrolase domain; family 43
(20)
Clostridium acetobutylicum atcc 824. Organism_taxid: 272562. Strain: atcc 824.
(2)
1a
1y7bA01
A:2-326
1b
1y7bB01
B:2-326
1c
1y7bC01
C:2-326
1d
1y7bD01
D:2-326
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Clostridium acetobutylicum atcc 824. Organism_taxid: 272562. Strain: atcc 824.
(2)
2a
1y7bA02
A:327-535
2b
1y7bB02
B:327-535
2c
1y7bC02
C:327-535
2d
1y7bD02
D:327-535
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_43_1y7bD01 (D:4-302)
1b: PFAM_Glyco_hydro_43_1y7bD02 (D:4-302)
1c: PFAM_Glyco_hydro_43_1y7bD03 (D:4-302)
1d: PFAM_Glyco_hydro_43_1y7bD04 (D:4-302)
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Clan
:
B_Fructosidase
(34)
Family
:
Glyco_hydro_43
(11)
Clostridium acetobutylicum
(2)
1a
Glyco_hydro_43-1y7bD01
D:4-302
1b
Glyco_hydro_43-1y7bD02
D:4-302
1c
Glyco_hydro_43-1y7bD03
D:4-302
1d
Glyco_hydro_43-1y7bD04
D:4-302
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Asym.Unit (421 KB)
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