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Biol. Unit 2
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Asym.Unit (351 KB)
Biol.Unit 1 (177 KB)
Biol.Unit 2 (176 KB)
Biol.Unit 3 (344 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GH78 FAMILY RHAMNOSIDASE OF BACILLUS SP. GL1 AT 1.9 A
Authors
:
Z. Cui, B. Mikami, W. Hashimoto, K. Murata
Date
:
17 Jan 07 (Deposition) - 13 Nov 07 (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)
Biol. Unit 3: A,B (1x)
Keywords
:
Alpha Barrel, Rhamnosidase, Glycoside Hydrolase Family 78, Invertase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Cui, Y. Maruyama, B. Mikami, W. Hashimoto, K. Murata
Crystal Structure Of Glycoside Hydrolase Family 78 Alpha-L-Rhamnosidase From Bacillus Sp. Gl1
J. Mol. Biol. V. 374 384 2007
[
close entry info
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Hetero Components
(1, 22)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: GLYCEROL (GOLa)
2aa: GLYCEROL (GOLaa)
2ab: GLYCEROL (GOLab)
2ac: GLYCEROL (GOLac)
2ad: GLYCEROL (GOLad)
2ae: GLYCEROL (GOLae)
2af: GLYCEROL (GOLaf)
2ag: GLYCEROL (GOLag)
2ah: GLYCEROL (GOLah)
2ai: GLYCEROL (GOLai)
2aj: GLYCEROL (GOLaj)
2ak: GLYCEROL (GOLak)
2al: GLYCEROL (GOLal)
2am: GLYCEROL (GOLam)
2an: GLYCEROL (GOLan)
2ao: GLYCEROL (GOLao)
2ap: GLYCEROL (GOLap)
2aq: GLYCEROL (GOLaq)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
2z: GLYCEROL (GOLz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
22
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(30, 30)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC5 (SOFTWARE)
08: BC6 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC4 (SOFTWARE)
14: CC6 (SOFTWARE)
15: CC7 (SOFTWARE)
16: CC8 (SOFTWARE)
17: CC9 (SOFTWARE)
18: DC1 (SOFTWARE)
19: DC2 (SOFTWARE)
20: DC5 (SOFTWARE)
21: DC6 (SOFTWARE)
22: DC9 (SOFTWARE)
23: EC2 (SOFTWARE)
24: EC4 (SOFTWARE)
25: EC5 (SOFTWARE)
26: EC6 (SOFTWARE)
27: EC7 (SOFTWARE)
28: EC9 (SOFTWARE)
29: FC1 (SOFTWARE)
30: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
GLU A:946 , LYS B:953 , GOL B:3041 , HOH B:4705 , HOH B:4874 , HOH B:4875
BINDING SITE FOR RESIDUE CA B 4002
02
AC3
SOFTWARE
VAL B:423 , HIS B:522 , GOL B:3042 , HOH B:4700 , HOH B:4701 , HOH B:4702
BINDING SITE FOR RESIDUE CA B 4003
03
AC4
SOFTWARE
LYS A:953 , GOL A:3039 , GOL A:3043 , GLU B:946 , HOH B:4704
BINDING SITE FOR RESIDUE CA A 4004
04
AC9
SOFTWARE
GLN B:58 , VAL B:59 , GLY B:60 , GLU B:200 , ARG B:527 , HOH B:4413
BINDING SITE FOR RESIDUE GOL B 3005
05
BC1
SOFTWARE
SER A:542 , TRP A:900 , HOH A:4111 , HOH A:4317 , HOH A:4736 , HOH A:4737 , LEU B:545 , GLY B:829
BINDING SITE FOR RESIDUE GOL A 3006
06
BC4
SOFTWARE
LEU A:545 , GLY A:829 , SER B:542 , TRP B:900 , HOH B:4422
BINDING SITE FOR RESIDUE GOL B 3009
07
BC5
SOFTWARE
TRP B:163 , TYR B:497 , VAL B:498 , HOH B:4254 , HOH B:4449 , HOH B:4611 , HOH B:4727
BINDING SITE FOR RESIDUE GOL B 3010
08
BC6
SOFTWARE
ILE B:798 , ASN B:827 , GLN B:830 , TYR B:843 , GOL B:3020 , HOH B:4574 , HOH B:4793
BINDING SITE FOR RESIDUE GOL B 3011
09
BC7
SOFTWARE
LEU B:223 , GLY B:265 , VAL B:266 , ARG B:267 , SER B:314 , HIS B:315 , PHE B:316 , HOH B:4317
BINDING SITE FOR RESIDUE GOL B 3012
10
BC8
SOFTWARE
TRP B:403 , HOH B:4304 , HOH B:4503
BINDING SITE FOR RESIDUE GOL B 3013
11
BC9
SOFTWARE
ASP B:567 , GLU B:572 , TRP B:576 , ASP B:579 , TRP B:629 , ARG B:858 , HIS B:862 , TRP B:864 , GOL B:3025 , HOH B:4097
BINDING SITE FOR RESIDUE GOL B 3014
12
CC2
SOFTWARE
THR B:279 , GLU B:280 , TRP B:281 , HOH B:4713
BINDING SITE FOR RESIDUE GOL B 3016
13
CC4
SOFTWARE
TYR B:245 , SER B:269 , TYR B:364 , ARG B:365 , PRO B:368 , GLU B:369
BINDING SITE FOR RESIDUE GOL B 3018
14
CC6
SOFTWARE
MET B:764 , GLN B:797 , ILE B:798 , ASP B:823 , ARG B:826 , ASN B:827 , GOL B:3011 , HOH B:4095
BINDING SITE FOR RESIDUE GOL B 3020
15
CC7
SOFTWARE
GLU A:425 , SER B:75 , ARG B:193 , ILE B:195 , PHE B:197 , HOH B:4204 , HOH B:4720
BINDING SITE FOR RESIDUE GOL B 3021
16
CC8
SOFTWARE
SER A:75 , ARG A:193 , ILE A:195 , PRO A:196 , PHE A:197 , HOH A:4109 , HOH A:4665 , GLU B:425
BINDING SITE FOR RESIDUE GOL A 3022
17
CC9
SOFTWARE
GLU A:201 , HOH A:4113 , TYR B:204 , PRO B:205 , HOH B:4132
BINDING SITE FOR RESIDUE GOL A 3023
18
DC1
SOFTWARE
PRO A:205 , ALA A:206 , GLU B:201 , GLN B:528 , ARG B:558 , HOH B:4124 , HOH B:4403
BINDING SITE FOR RESIDUE GOL B 3024
19
DC2
SOFTWARE
PHE B:102 , GLN B:147 , GLU B:572 , TRP B:576 , ASN B:849 , ARG B:858 , GOL B:3014
BINDING SITE FOR RESIDUE GOL B 3025
20
DC5
SOFTWARE
GLU B:70 , VAL B:191 , ASN B:602 , HOH B:4238
BINDING SITE FOR RESIDUE GOL B 3028
21
DC6
SOFTWARE
GLY B:28 , SER B:29 , ALA B:128 , ARG B:130 , HOH B:4877
BINDING SITE FOR RESIDUE GOL B 3029
22
DC9
SOFTWARE
ARG A:327 , ARG B:157 , GLU B:158 , LEU B:159 , ARG B:491 , HOH B:4849
BINDING SITE FOR RESIDUE GOL B 3032
23
EC2
SOFTWARE
ARG B:213 , ARG B:410 , PHE B:432 , GLU B:433 , ASP B:434 , HOH B:4878
BINDING SITE FOR RESIDUE GOL B 3034
24
EC4
SOFTWARE
ARG B:447 , HIS B:555 , HOH B:4092 , HOH B:4105
BINDING SITE FOR RESIDUE GOL B 3036
25
EC5
SOFTWARE
PHE B:631 , ILE B:634 , LEU B:635 , PHE B:701 , LYS B:704 , ALA B:705 , ASP B:708
BINDING SITE FOR RESIDUE GOL B 3037
26
EC6
SOFTWARE
PRO A:353 , THR B:342 , LYS B:385 , HOH B:4489 , HOH B:4514
BINDING SITE FOR RESIDUE GOL B 3038
27
EC7
SOFTWARE
GLU A:933 , LYS A:953 , TYR A:954 , GOL A:3043 , CA A:4004 , GLU B:946 , HOH B:4392
BINDING SITE FOR RESIDUE GOL A 3039
28
EC9
SOFTWARE
GLU A:946 , HOH A:4569 , GLU B:933 , LYS B:953 , TYR B:954 , MET B:955 , CA B:4002 , HOH B:4714 , HOH B:4802 , HOH B:4874
BINDING SITE FOR RESIDUE GOL B 3041
29
FC1
SOFTWARE
VAL B:423 , PRO B:424 , HIS B:522 , GLU B:523 , CA B:4003 , HOH B:4160 , HOH B:4701
BINDING SITE FOR RESIDUE GOL B 3042
30
FC2
SOFTWARE
VAL A:952 , LYS A:953 , TYR A:954 , GOL A:3039 , CA A:4004 , HOH A:4580 , HOH A:4812 , GLU B:946 , HOH B:4704
BINDING SITE FOR RESIDUE GOL A 3043
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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
View:
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
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Bac_rhamnosid_2okxB01 (B:431-941)
1b: PFAM_Bac_rhamnosid_2okxB02 (B:431-941)
2a: PFAM_Bac_rhamnosid_N_2okxB03 (B:35-210)
2b: PFAM_Bac_rhamnosid_N_2okxB04 (B:35-210)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
Bac_rhamnosid
(1)
Bacillus sp. (strain GL1)
(1)
1a
Bac_rhamnosid-2okxB01
B:431-941
1b
Bac_rhamnosid-2okxB02
B:431-941
Clan
:
GBD
(153)
Family
:
Bac_rhamnosid_N
(1)
Bacillus sp. (strain GL1)
(1)
2a
Bac_rhamnosid_N-2okxB03
B:35-210
2b
Bac_rhamnosid_N-2okxB04
B:35-210
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