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3LRM
Asym. Unit
Info
Asym.Unit (317 KB)
Biol.Unit 1 (307 KB)
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(1)
Title
:
STRUCTURE OF ALFA-GALACTOSIDASE FROM SACCHAROMYCES CEREVISIAE WITH RAFFINOSE
Authors
:
R. Fernandez-Leiro, A. Pereira-Rodriguez, M. E. Cerdan, M. Becerra, J Aparicio
Date
:
11 Feb 10 (Deposition) - 30 Jun 10 (Release) - 26 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Alpha-Galactosidase, Tetramer, Gh27, Raffinose, Glycoprotein, Glycosidase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Fernandez-Leiro, A. Pereira-Rodriguez, M. E. Cerdan, M. Becerra, J. Sanz-Aparicio
Structural Analysis Of Saccharomyces Cerevisiae Alpha-Galactosidase And Its Complexes With Natural Substrates Reveals New Insights Into Substrate Specificity Of Gh27 Glycosidases.
J. Biol. Chem. V. 285 28020 2010
[
close entry info
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Hetero Components
(3, 29)
Info
All Hetero Components
1a: ALPHA D-GALACTOSE (GLAa)
1b: ALPHA D-GALACTOSE (GLAb)
1c: ALPHA D-GALACTOSE (GLAc)
1d: ALPHA D-GALACTOSE (GLAd)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
2m: N-ACETYL-D-GLUCOSAMINE (NAGm)
2n: N-ACETYL-D-GLUCOSAMINE (NAGn)
2o: N-ACETYL-D-GLUCOSAMINE (NAGo)
2p: N-ACETYL-D-GLUCOSAMINE (NAGp)
2q: N-ACETYL-D-GLUCOSAMINE (NAGq)
2r: N-ACETYL-D-GLUCOSAMINE (NAGr)
2s: N-ACETYL-D-GLUCOSAMINE (NAGs)
2t: N-ACETYL-D-GLUCOSAMINE (NAGt)
2u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3a: SUCROSE (SUCa)
3b: SUCROSE (SUCb)
3c: SUCROSE (SUCc)
3d: SUCROSE (SUCd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GLA
4
Ligand/Ion
ALPHA D-GALACTOSE
2
NAG
21
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SUC
4
Ligand/Ion
SUCROSE
[
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:175 , GLY A:178 , ARG A:179 , PRO A:180 , HOH A:504 , HOH A:558 , HOH A:1094 , HOH A:1460
BINDING SITE FOR RESIDUE NAG A 2001
02
AC2
SOFTWARE
GLY A:267 , GLY A:269 , ASN A:270 , NAG A:3002 , ASN B:381 , LEU B:382
BINDING SITE FOR RESIDUE NAG A 3001
03
AC3
SOFTWARE
ASN A:298 , HOH A:557 , HOH A:563 , HOH A:1414 , HOH A:1452 , HOH A:1533 , NAG A:3001
BINDING SITE FOR RESIDUE NAG A 3002
04
AC4
SOFTWARE
ASP A:273 , SER A:302 , ASN A:403 , HOH A:533
BINDING SITE FOR RESIDUE NAG A 4001
05
AC5
SOFTWARE
ASP A:63 , THR A:417 , ASN A:422 , GLU A:425 , NAG A:5002
BINDING SITE FOR RESIDUE NAG A 5001
06
AC6
SOFTWARE
HOH A:530 , HOH A:1415 , NAG A:5001
BINDING SITE FOR RESIDUE NAG A 5002
07
AC7
SOFTWARE
TRP A:37 , CYS A:121 , TRP A:188 , ASP A:209 , HOH A:548 , HOH A:1361 , HOH A:1481 , GLA A:9002 , VAL B:19 , GLN B:251 , HOH B:551
BINDING SITE FOR RESIDUE SUC A 9001
08
AC8
SOFTWARE
TRP A:37 , ASP A:72 , ASP A:73 , TYR A:113 , CYS A:121 , LYS A:147 , CYS A:186 , TRP A:188 , ARG A:205 , ASP A:209 , HOH A:1299 , SUC A:9001
BINDING SITE FOR RESIDUE GLA A 9002
09
AC9
SOFTWARE
ASN B:175 , GLY B:178 , ARG B:179 , HOH B:541 , HOH B:1158
BINDING SITE FOR RESIDUE NAG B 2001
10
BC1
SOFTWARE
GLY B:269 , ASN B:270 , HOH B:1060 , HOH B:1680 , NAG B:3002 , LEU C:382
BINDING SITE FOR RESIDUE NAG B 3001
11
BC2
SOFTWARE
ASN B:298 , NAG B:3001
BINDING SITE FOR RESIDUE NAG B 3002
12
BC3
SOFTWARE
SER B:302 , ASN B:403 , HOH B:492 , HOH B:1302
BINDING SITE FOR RESIDUE NAG B 4001
13
BC4
SOFTWARE
ASP B:63 , THR B:417 , ASN B:422 , GLU B:425 , HOH B:1195 , HOH B:1388 , NAG B:5002
BINDING SITE FOR RESIDUE NAG B 5001
14
BC5
SOFTWARE
HOH B:1388 , NAG B:5001
BINDING SITE FOR RESIDUE NAG B 5002
15
BC6
SOFTWARE
TRP B:37 , CYS B:121 , ASP B:209 , GLY B:234 , PHE B:235 , HOH B:1232 , HOH B:1497 , GLA B:9002 , VAL C:19 , GLN C:251
BINDING SITE FOR RESIDUE SUC B 9001
16
BC7
SOFTWARE
TRP B:37 , ASP B:72 , ASP B:73 , TYR B:113 , CYS B:121 , LYS B:147 , CYS B:186 , ARG B:205 , ASP B:209 , SUC B:9001
BINDING SITE FOR RESIDUE GLA B 9002
17
BC8
SOFTWARE
GLU A:89 , ASN C:175 , GLY C:178 , ARG C:179 , HOH C:1374
BINDING SITE FOR RESIDUE NAG C 2001
18
BC9
SOFTWARE
GLY C:267 , GLY C:269 , ASN C:270 , HOH C:1137 , NAG C:3002 , LEU D:382
BINDING SITE FOR RESIDUE NAG C 3001
19
CC1
SOFTWARE
ASN C:298 , HOH C:1197 , NAG C:3001
BINDING SITE FOR RESIDUE NAG C 3002
20
CC2
SOFTWARE
PRO A:368 , SER C:302 , ASN C:403 , HOH C:1156 , HOH C:1617
BINDING SITE FOR RESIDUE NAG C 4001
21
CC3
SOFTWARE
ASP C:63 , THR C:417 , ASN C:422 , HOH C:1209
BINDING SITE FOR RESIDUE NAG C 5001
22
CC4
SOFTWARE
TRP C:37 , CYS C:121 , TRP C:188 , ASP C:209 , GLY C:234 , PHE C:235 , HOH C:499 , HOH C:540 , GLA C:9002 , VAL D:19 , GLN D:251
BINDING SITE FOR RESIDUE SUC C 9001
23
CC5
SOFTWARE
TRP C:37 , ASP C:72 , ASP C:73 , TYR C:113 , CYS C:121 , LYS C:147 , CYS C:186 , TRP C:188 , ARG C:205 , ASP C:209 , HOH C:1411 , HOH C:1493 , SUC C:9001
BINDING SITE FOR RESIDUE GLA C 9002
24
CC6
SOFTWARE
ASN D:175 , GLY D:178 , ARG D:179 , PRO D:180 , HOH D:494 , HOH D:1444 , HOH D:1538
BINDING SITE FOR RESIDUE NAG D 2001
25
CC7
SOFTWARE
GLU D:132 , ASP D:273 , SER D:302 , ASN D:403 , HOH D:1099 , HOH D:1237 , HOH D:1250
BINDING SITE FOR RESIDUE NAG D 4001
26
CC8
SOFTWARE
ASP D:63 , THR D:417 , ASN D:422 , GLU D:425 , HOH D:1544 , NAG D:5002
BINDING SITE FOR RESIDUE NAG D 5001
27
CC9
SOFTWARE
THR D:424 , HOH D:535 , HOH D:1485 , HOH D:1544 , NAG D:5001
BINDING SITE FOR RESIDUE NAG D 5002
28
DC1
SOFTWARE
GLN A:251 , TRP D:37 , CYS D:121 , TRP D:188 , ASP D:209 , GLY D:234 , PHE D:235 , HOH D:541 , HOH D:1489 , GLA D:9002
BINDING SITE FOR RESIDUE SUC D 9001
29
DC2
SOFTWARE
TRP D:37 , ASP D:72 , ASP D:73 , TYR D:113 , CYS D:121 , LYS D:147 , CYS D:186 , TRP D:188 , ARG D:205 , ASP D:209 , SUC D:9001
BINDING SITE FOR RESIDUE GLA D 9002
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ALPHA_GALACTOSIDASE (A:65-80,B:65-80,C:65-80,D:65-80)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALPHA_GALACTOSIDASE
PS00512
Alpha-galactosidase signature.
MEL1_YEASX
65-80
4
A:65-80
B:65-80
C:65-80
D:65-80
[
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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
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Melibiase_3lrmD01 (D:19-363)
1b: PFAM_Melibiase_3lrmD02 (D:19-363)
1c: PFAM_Melibiase_3lrmD03 (D:19-363)
1d: PFAM_Melibiase_3lrmD04 (D:19-363)
View:
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Clans
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(
)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Melibiase
(11)
Saccharomyces cerevisiae (Bakers yeast)
(3)
1a
Melibiase-3lrmD01
D:19-363
1b
Melibiase-3lrmD02
D:19-363
1c
Melibiase-3lrmD03
D:19-363
1d
Melibiase-3lrmD04
D:19-363
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