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3A21
Biol. Unit 2
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
)
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Hetero Components
(4, 19)
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
2
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
13
Ligand/Ion
GLYCEROL
4
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(28, 28)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC5 (SOFTWARE)
08: BC6 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC2 (SOFTWARE)
11: CC3 (SOFTWARE)
12: CC4 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC6 (SOFTWARE)
15: CC7 (SOFTWARE)
16: CC8 (SOFTWARE)
17: CC9 (SOFTWARE)
18: DC1 (SOFTWARE)
19: DC2 (SOFTWARE)
20: DC3 (SOFTWARE)
21: DC4 (SOFTWARE)
22: DC5 (SOFTWARE)
23: DC6 (SOFTWARE)
24: DC7 (SOFTWARE)
25: DC8 (SOFTWARE)
26: DC9 (SOFTWARE)
27: EC1 (SOFTWARE)
28: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
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
04
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
05
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
06
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
07
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
08
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
09
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
10
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
11
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
12
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
13
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
14
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
15
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
16
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
17
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
18
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
19
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
20
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
21
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
22
DC5
SOFTWARE
SER B:256 , MET B:257 , THR B:258 , HOH B:1230 , HOH B:1660
BINDING SITE FOR RESIDUE GOL B 933
23
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
24
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
25
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
26
DC9
SOFTWARE
ARG B:471 , GLY B:516 , HOH B:694 , HOH B:1085 , HOH B:1591
BINDING SITE FOR RESIDUE SO4 B 972
27
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
28
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 only available for the asymmetric unit)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
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[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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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)
View:
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Classes
(
)
(
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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)
Info
all PFAM domains
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Chain B
Asymmetric Unit 1
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