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3A22
Asym. Unit
Info
Asym.Unit (225 KB)
Biol.Unit 1 (113 KB)
Biol.Unit 2 (112 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BETA-L-ARABINOPYRANOSIDASE COMPLEXED WITH L-ARABINOSE
Authors
:
Z. Fujimoto, H. Ichinose, S. Kaneko
Date
:
27 Apr 09 (Deposition) - 14 Jul 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Beta-Alpha-Barrel, Greek Key Motif, Beta-Jellyroll, Beta-Trefoil, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ichinose, Z. Fujimoto, M. Honda, K. Harazono, Y. Nishimoto, A. Uzura, S. Kaneko
A Beta-L-Arabinopyranosidase From Streptomyces Avermitilis Is A Novel Member Of Glycoside Hydrolase Family 27.
J. Biol. Chem. V. 284 25097 2009
(for further references see the
PDB file header
)
[
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]
Hetero Components
(5, 35)
Info
All Hetero Components
1a: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGa)
1b: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGb)
1c: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGc)
1d: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGd)
2a: ALPHA-L-ARABINOSE (ARAa)
2b: ALPHA-L-ARABINOSE (ARAb)
2c: ALPHA-L-ARABINOSE (ARAc)
2d: ALPHA-L-ARABINOSE (ARAd)
2e: ALPHA-L-ARABINOSE (ARAe)
2f: ALPHA-L-ARABINOSE (ARAf)
2g: ALPHA-L-ARABINOSE (ARAg)
2h: ALPHA-L-ARABINOSE (ARAh)
2i: ALPHA-L-ARABINOSE (ARAi)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
4n: GLYCEROL (GOLn)
4o: GLYCEROL (GOLo)
4p: GLYCEROL (GOLp)
4q: GLYCEROL (GOLq)
4r: GLYCEROL (GOLr)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PG
4
Ligand/Ion
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2
ARA
9
Ligand/Ion
ALPHA-L-ARABINOSE
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
GOL
18
Ligand/Ion
GLYCEROL
5
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:63 , ASP A:98 , GLU A:99 , TYR A:140 , CYS A:148 , LYS A:184 , ASP A:186 , CYS A:224 , TRP A:226 , ARG A:243 , ASP A:247 , MET A:283 , HOH A:827 , GOL A:919
BINDING SITE FOR RESIDUE ARA A 701
02
AC2
SOFTWARE
HOH A:22 , THR A:481 , ASP A:545 , ILE A:546 , TYR A:547 , ASN A:548 , TRP A:560 , ASN A:563 , ASN A:567 , GLN A:568 , HOH A:1178
BINDING SITE FOR RESIDUE ARA A 711
03
AC3
SOFTWARE
ASP A:587 , ALA A:588 , TYR A:589 , ASN A:590 , TRP A:602 , ASN A:605 , GLN A:607 , ASN A:609 , HOH A:1177 , ASN B:553 , TRP B:602
BINDING SITE FOR RESIDUE ARA A 721
04
AC4
SOFTWARE
ASP A:630 , ALA A:631 , TYR A:632 , ASN A:633 , TRP A:645 , THR A:649 , ASN A:652 , HOH A:1035 , HOH A:1074
BINDING SITE FOR RESIDUE ARA A 731
05
AC5
SOFTWARE
TYR A:547 , GLU A:558 , HOH A:976
BINDING SITE FOR RESIDUE ARA A 741
06
AC6
SOFTWARE
LYS A:346 , GLU A:349 , THR A:352 , ARG A:575 , GLU A:577 , HOH A:1003
BINDING SITE FOR RESIDUE GOL A 911
07
AC7
SOFTWARE
ARG A:49 , THR A:490 , GLY A:491 , ALA A:492 , SER A:493 , HIS B:131 , GLY B:134 , LEU B:135 , HOH B:1092 , HOH B:1240
BINDING SITE FOR RESIDUE GOL A 912
08
AC8
SOFTWARE
TRP A:232 , ASN A:233 , THR A:271 , THR A:481 , ALA A:482 , ASN A:549 , HOH A:671 , HOH A:886 , HOH A:940 , HOH A:974
BINDING SITE FOR RESIDUE GOL A 914
09
AC9
SOFTWARE
ALA A:348 , GLU A:349 , ASP A:350 , THR A:351 , LEU A:354 , ILE A:381 , THR A:382 , HOH A:678 , HOH A:1247
BINDING SITE FOR RESIDUE GOL A 915
10
BC1
SOFTWARE
THR A:411 , GLY A:412 , TYR A:413 , THR A:414 , HOH A:939 , SO4 A:971 , ALA B:393 , SER B:394
BINDING SITE FOR RESIDUE GOL A 917
11
BC2
SOFTWARE
CYS A:148 , TYR A:152 , CYS A:188 , TRP A:226 , ASP A:247 , TYR A:250 , ARA A:701 , HOH A:1004 , HOH A:1300 , THR B:593 , HOH B:747
BINDING SITE FOR RESIDUE GOL A 919
12
BC3
SOFTWARE
GLY A:209 , ALA A:212 , PRO A:218 , LEU A:219 , HOH A:758 , HOH A:852 , HOH A:1258
BINDING SITE FOR RESIDUE GOL A 925
13
BC4
SOFTWARE
THR A:258 , SER A:259 , SER A:262 , HOH A:1038 , HOH A:1261 , LEU B:591 , HOH B:1189
BINDING SITE FOR RESIDUE GOL A 926
14
BC5
SOFTWARE
SER A:504 , CYS A:562 , HOH A:712 , HOH A:887
BINDING SITE FOR RESIDUE GOL A 927
15
BC6
SOFTWARE
SER A:493 , ALA A:494 , HOH A:759 , LYS B:136
BINDING SITE FOR RESIDUE GOL A 930
16
BC7
SOFTWARE
TYR A:72 , PRO A:120 , GLY A:436 , TYR A:438 , THR A:450 , HOH A:978 , HOH A:1051 , HOH A:1361 , ASN B:466
BINDING SITE FOR RESIDUE 1PG A 962
17
BC8
SOFTWARE
PRO A:153 , TYR A:251 , ASN A:253 , HOH A:1146 , VAL B:623 , ALA B:625 , GLY B:626
BINDING SITE FOR RESIDUE 1PG A 964
18
BC9
SOFTWARE
SER A:409 , ALA A:410 , THR A:411 , HOH A:772 , GOL A:917 , HOH A:1053 , ALA B:393 , THR B:431 , HOH B:915 , HOH B:1207
BINDING SITE FOR RESIDUE SO4 A 971
19
CC1
SOFTWARE
ARG A:471 , PRO A:517 , ALA A:518 , HOH A:740
BINDING SITE FOR RESIDUE SO4 A 973
20
CC2
SOFTWARE
TRP B:63 , ASP B:98 , GLU B:99 , TYR B:140 , CYS B:148 , LYS B:184 , ASP B:186 , CYS B:224 , TRP B:226 , ARG B:243 , ASP B:247 , MET B:283 , HOH B:716 , GOL B:928
BINDING SITE FOR RESIDUE ARA B 751
21
CC3
SOFTWARE
THR B:481 , ASP B:545 , ILE B:546 , TYR B:547 , ASN B:548 , TRP B:560 , ASN B:563 , ASN B:567 , HOH B:736 , HOH B:750
BINDING SITE FOR RESIDUE ARA B 761
22
CC4
SOFTWARE
ASN A:553 , TRP A:602 , ASP B:587 , TYR B:589 , ASN B:590 , LEU B:591 , TRP B:602 , ASN B:605 , GLN B:607 , ASN B:609
BINDING SITE FOR RESIDUE ARA B 771
23
CC5
SOFTWARE
ASP B:630 , ALA B:631 , TYR B:632 , ASN B:633 , TRP B:645 , THR B:649 , ASN B:652 , 1PG B:966 , HOH B:1036 , HOH B:1065
BINDING SITE FOR RESIDUE ARA B 781
24
CC6
SOFTWARE
ALA B:348 , GLU B:349 , ASP B:350 , THR B:351 , LEU B:354 , ILE B:381 , THR B:382 , HOH B:860 , HOH B:1178
BINDING SITE FOR RESIDUE GOL B 913
25
CC7
SOFTWARE
THR A:292 , HOH A:803 , THR B:320 , SER B:321 , GLU B:322 , HOH B:1351
BINDING SITE FOR RESIDUE GOL B 916
26
CC8
SOFTWARE
GLU B:349 , THR B:352 , ARG B:575 , GLU B:577 , GLY B:582 , CYS B:604 , HOH B:1016 , HOH B:1256
BINDING SITE FOR RESIDUE GOL B 918
27
CC9
SOFTWARE
ASP B:71 , TYR B:72 , SER B:73 , GLU B:118 , PRO B:120 , LYS B:505 , 1PG B:963 , HOH B:1131 , HOH B:1135
BINDING SITE FOR RESIDUE GOL B 920
28
DC1
SOFTWARE
PRO B:54 , THR B:275 , GLY B:276 , HOH B:782 , HOH B:783 , HOH B:784 , HOH B:894
BINDING SITE FOR RESIDUE GOL B 922
29
DC2
SOFTWARE
THR A:593 , TYR B:152 , CYS B:188 , ASP B:247 , TYR B:250 , ARA B:751 , HOH B:823 , HOH B:1308
BINDING SITE FOR RESIDUE GOL B 928
30
DC3
SOFTWARE
GLY A:166 , HIS A:167 , TYR A:168 , ASP A:169 , HOH A:1016 , HOH A:1263 , HOH B:1096
BINDING SITE FOR RESIDUE GOL B 932
31
DC4
SOFTWARE
SER B:256 , MET B:257 , THR B:258 , HOH B:1180
BINDING SITE FOR RESIDUE GOL B 934
32
DC5
SOFTWARE
ALA A:294 , ARG A:297 , GLU A:322 , ALA B:85 , LEU B:316 , MET B:319 , SER B:321 , ALA B:324 , LYS B:328 , HOH B:738 , HOH B:757 , HOH B:1073 , HOH B:1114
BINDING SITE FOR RESIDUE EPE B 951
33
DC6
SOFTWARE
TYR B:72 , PRO B:120 , ALA B:434 , GLY B:435 , THR B:450 , GOL B:920 , HOH B:1055
BINDING SITE FOR RESIDUE 1PG B 963
34
DC7
SOFTWARE
ALA A:192 , ARG A:542 , HOH A:723 , HOH A:1032 , ASN B:595 , TYR B:632 , ASN B:633 , TRP B:645 , ARA B:781 , HOH B:1005 , HOH B:1007
BINDING SITE FOR RESIDUE 1PG B 966
35
DC8
SOFTWARE
ARG B:471 , GLY B:515 , GLY B:516 , HOH B:694 , HOH B:1386 , HOH B:1387
BINDING SITE FOR RESIDUE SO4 B 972
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3a22B01 (B:47-339)
1b: CATH_3a22A01 (A:45-339)
2a: CATH_3a22A04 (A:532-658)
2b: CATH_3a22B04 (B:532-658)
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(
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Streptomyces avermitilis. Organism_taxid: 33903. Strain: nbrc14893.
(3)
1a
3a22B01
B:47-339
1b
3a22A01
A:45-339
Class
:
Mainly Beta
(13760)
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
Streptomyces avermitilis. Organism_taxid: 33903. Strain: nbrc14893.
(3)
2a
3a22A04
A:532-658
2b
3a22B04
B:532-658
[
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Pfam Domains
(0, 0)
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Asym.Unit (225 KB)
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