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3A21
Asym. Unit
Info
Asym.Unit (235 KB)
Biol.Unit 1 (118 KB)
Biol.Unit 2 (117 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF STREPTOMYCES AVERMITILIS BETA-L-ARABINOPYRANOSIDASE
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
:
1.51
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
)
[
close entry info
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Hetero Components
(4, 38)
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: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
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)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
3r: GLYCEROL (GOLr)
3s: GLYCEROL (GOLs)
3t: GLYCEROL (GOLt)
3u: GLYCEROL (GOLu)
3v: GLYCEROL (GOLv)
3w: GLYCEROL (GOLw)
3x: GLYCEROL (GOLx)
3y: GLYCEROL (GOLy)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
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
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
GOL
25
Ligand/Ion
GLYCEROL
4
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(38, 38)
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)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:22 , THR A:481 , ASP A:545 , TYR A:547 , ASN A:548 , TRP A:560 , ASN A:563 , ASN A:567 , HOH A:1222
BINDING SITE FOR RESIDUE GOL A 901
02
AC2
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:1053 , TRP B:602
BINDING SITE FOR RESIDUE GOL A 902
03
AC3
SOFTWARE
ASP A:630 , ALA A:631 , TYR A:632 , ASN A:633 , TRP A:645 , ASN A:652 , HOH A:1009
BINDING SITE FOR RESIDUE GOL A 903
04
AC4
SOFTWARE
LYS A:346 , GLU A:349 , THR A:352 , ARG A:575 , GLU A:577 , GLY A:582 , CYS A:604 , GOL A:921 , HOH A:1414
BINDING SITE FOR RESIDUE GOL A 911
05
AC5
SOFTWARE
ARG A:49 , THR A:490 , GLY A:491 , ALA A:492 , SER A:493 , HOH A:904 , HIS B:131 , GLY B:134 , LEU B:135 , HOH B:910 , HOH B:1093
BINDING SITE FOR RESIDUE GOL A 912
06
AC6
SOFTWARE
TRP A:232 , ASN A:233 , THR A:271 , THR A:481 , ALA A:482 , ASN A:549 , HOH A:671 , HOH A:892 , HOH A:949 , HOH A:1347
BINDING SITE FOR RESIDUE GOL A 914
07
AC7
SOFTWARE
ALA A:348 , GLU A:349 , ASP A:350 , THR A:351 , LEU A:354 , ILE A:381 , THR A:382 , HOH A:1163 , HOH A:1303
BINDING SITE FOR RESIDUE GOL A 915
08
AC8
SOFTWARE
THR A:411 , GLY A:412 , TYR A:413 , THR A:414 , HOH A:936 , SO4 A:971 , ASN B:392 , ALA B:393 , SER B:394
BINDING SITE FOR RESIDUE GOL A 917
09
AC9
SOFTWARE
TYR A:152 , TRP A:226 , THR A:246 , ASP A:247 , TYR A:250 , HOH A:746 , HOH A:1016 , THR B:593
BINDING SITE FOR RESIDUE GOL A 919
10
BC1
SOFTWARE
GLN A:355 , ARG A:374 , ASN A:583 , ASP A:603 , CYS A:604 , HOH A:890 , GOL A:911 , HOH A:1171 , HOH A:1588
BINDING SITE FOR RESIDUE GOL A 921
11
BC2
SOFTWARE
GLY A:209 , ALA A:212 , PRO A:218 , LEU A:219 , HOH A:757 , HOH A:857 , HOH A:1316 , HOH A:1375
BINDING SITE FOR RESIDUE GOL A 925
12
BC3
SOFTWARE
THR A:258 , SER A:259 , SER A:262 , HOH A:1075 , HOH A:1117 , LEU B:591 , HOH B:1217
BINDING SITE FOR RESIDUE GOL A 926
13
BC4
SOFTWARE
TYR A:72 , PRO A:120 , GLY A:121 , GLY A:435 , GLY A:436 , TYR A:438 , THR A:450 , HOH A:1027 , HOH A:1348 , ASN B:466
BINDING SITE FOR RESIDUE 1PG A 962
14
BC5
SOFTWARE
PRO A:153 , TYR A:251 , ASN A:253 , HOH A:1118 , VAL B:623 , ALA B:625 , GLY B:626
BINDING SITE FOR RESIDUE 1PG A 964
15
BC6
SOFTWARE
SER A:409 , ALA A:410 , THR A:411 , HOH A:771 , GOL A:917 , HOH A:1018 , HOH A:1412 , ALA B:393 , HOH B:912 , HOH B:1238
BINDING SITE FOR RESIDUE SO4 A 971
16
BC7
SOFTWARE
ARG A:471 , GLY A:516 , HOH A:681 , HOH A:810 , HOH A:1005
BINDING SITE FOR RESIDUE SO4 A 975
17
BC8
SOFTWARE
ARG A:471 , PRO A:517 , ALA A:518 , HOH A:739 , HOH A:1459
BINDING SITE FOR RESIDUE SO4 A 976
18
BC9
SOFTWARE
GLY A:166 , HIS A:167 , TYR A:168 , ASP A:169 , HOH A:726 , HOH A:861 , HOH A:1111 , GOL B:931
BINDING SITE FOR RESIDUE SO4 A 977
19
CC1
SOFTWARE
ARG A:297 , ILE A:326 , TRP A:401 , HOH A:765 , HOH A:858 , HOH A:1279 , HOH A:1450
BINDING SITE FOR RESIDUE SO4 A 978
20
CC2
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:738 , HOH B:749
BINDING SITE FOR RESIDUE GOL B 904
21
CC3
SOFTWARE
TRP A:602 , ASP B:587 , TYR B:589 , ASN B:590 , TRP B:602 , ASN B:605 , GLN B:607 , ASN B:609
BINDING SITE FOR RESIDUE GOL B 905
22
CC4
SOFTWARE
ASP B:630 , ALA B:631 , TYR B:632 , ASN B:633 , TRP B:645 , ASN B:652 , HOH B:1237
BINDING SITE FOR RESIDUE GOL B 906
23
CC5
SOFTWARE
ALA B:348 , ASP B:350 , THR B:351 , LEU B:354 , ILE B:381 , THR B:382 , HOH B:858 , HOH B:859 , HOH B:1199
BINDING SITE FOR RESIDUE GOL B 913
24
CC6
SOFTWARE
THR A:292 , HOH A:799 , HOH A:801 , THR B:320 , SER B:321 , GLU B:322 , HOH B:1427
BINDING SITE FOR RESIDUE GOL B 916
25
CC7
SOFTWARE
LYS B:346 , GLU B:349 , THR B:352 , THR B:573 , ARG B:575 , GLU B:577 , GLY B:582 , GOL B:924
BINDING SITE FOR RESIDUE GOL B 918
26
CC8
SOFTWARE
ASP B:71 , TYR B:72 , SER B:73 , ALA B:117 , GLU B:118 , LYS B:505 , HOH B:1092 , HOH B:1132
BINDING SITE FOR RESIDUE GOL B 920
27
CC9
SOFTWARE
GLN B:355 , ARG B:374 , ASN B:583 , ASP B:603 , CYS B:604 , HOH B:705 , GOL B:918 , HOH B:1242 , HOH B:1440
BINDING SITE FOR RESIDUE GOL B 924
28
DC1
SOFTWARE
THR A:593 , HOH A:960 , TYR B:152 , TRP B:226 , THR B:246 , ASP B:247 , TYR B:250 , HOH B:821 , HOH B:1046
BINDING SITE FOR RESIDUE GOL B 928
29
DC2
SOFTWARE
ALA A:45 , VAL A:46 , GLY B:209 , PRO B:218 , LEU B:219 , HOH B:987 , HOH B:1143 , HOH B:1163
BINDING SITE FOR RESIDUE GOL B 929
30
DC3
SOFTWARE
ASN A:595 , HOH A:726 , SO4 A:977 , HOH A:1803 , ASP B:191 , ALA B:192 , HOH B:801 , HOH B:949
BINDING SITE FOR RESIDUE GOL B 931
31
DC4
SOFTWARE
TYR A:228 , GLY B:592 , THR B:594 , ASN B:595 , THR B:597 , HOH B:1006 , HOH B:1567 , HOH B:1680
BINDING SITE FOR RESIDUE GOL B 932
32
DC5
SOFTWARE
SER B:256 , MET B:257 , THR B:258 , HOH B:1230 , HOH B:1660
BINDING SITE FOR RESIDUE GOL B 933
33
DC6
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:737 , HOH B:756 , HOH B:1081 , HOH B:1113
BINDING SITE FOR RESIDUE EPE B 951
34
DC7
SOFTWARE
TYR B:72 , PRO B:120 , ALA B:434 , GLY B:435 , THR B:450 , ALA B:452 , HOH B:1024
BINDING SITE FOR RESIDUE 1PG B 963
35
DC8
SOFTWARE
VAL A:623 , ALA A:625 , GLY A:626 , TYR B:251 , GLY B:252 , ASN B:253 , HOH B:1332 , HOH B:1577
BINDING SITE FOR RESIDUE 1PG B 965
36
DC9
SOFTWARE
ARG B:471 , GLY B:516 , HOH B:694 , HOH B:1085 , HOH B:1591
BINDING SITE FOR RESIDUE SO4 B 972
37
EC1
SOFTWARE
GLY B:166 , HIS B:167 , TYR B:168 , ASP B:169 , GLN B:170 , SO4 B:974 , HOH B:1497
BINDING SITE FOR RESIDUE SO4 B 973
38
EC2
SOFTWARE
GLY B:166 , HIS B:167 , TYR B:168 , ASP B:169 , SO4 B:973 , HOH B:1124
BINDING SITE FOR RESIDUE SO4 B 974
[
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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_3a21B01 (B:47-339)
1b: CATH_3a21A01 (A:45-339)
2a: CATH_3a21A04 (A:532-658)
2b: CATH_3a21B04 (B:532-658)
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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
3a21B01
B:47-339
1b
3a21A01
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
3a21A04
A:532-658
2b
3a21B04
B:532-658
[
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]
Pfam Domains
(0, 0)
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Asym.Unit (235 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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