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4IIC
Asym. Unit
Info
Asym.Unit (322 KB)
Biol.Unit 1 (308 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BETA-GLUCOSIDASE 1 FROM ASPERGILLUS ACULEATUS IN COMPLEX WITH ISOFAGOMINE
Authors
:
K. Suzuki, J. Sumitani, T. Kawaguchi, S. Fushinobu
Date
:
20 Dec 12 (Deposition) - 10 Apr 13 (Release) - 12 Aug 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Tim Barrel, Hydrolase, High-Mannose N-Glycosylations, Extracellular
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Suzuki, J. Sumitani, Y. W. Nam, T. Nishimaki, S. Tani, T. Wakagi, T. Kawaguchi, S. Fushinobu
Crystal Structures Of Glycoside Hydrolase Family 3 Beta-Glucosidase 1 From Aspergillus Aculeatus
Biochem. J. V. 452 211 2013
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 94)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
1f: BETA-D-MANNOSE (BMAf)
1g: BETA-D-MANNOSE (BMAg)
1h: BETA-D-MANNOSE (BMAh)
1i: BETA-D-MANNOSE (BMAi)
1j: BETA-D-MANNOSE (BMAj)
1k: BETA-D-MANNOSE (BMAk)
1l: BETA-D-MANNOSE (BMAl)
1m: BETA-D-MANNOSE (BMAm)
2a: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPER... (IFMa)
2b: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPER... (IFMb)
3a: ALPHA-D-MANNOSE (MANa)
3aa: ALPHA-D-MANNOSE (MANaa)
3ab: ALPHA-D-MANNOSE (MANab)
3ac: ALPHA-D-MANNOSE (MANac)
3ad: ALPHA-D-MANNOSE (MANad)
3ae: ALPHA-D-MANNOSE (MANae)
3af: ALPHA-D-MANNOSE (MANaf)
3ag: ALPHA-D-MANNOSE (MANag)
3ah: ALPHA-D-MANNOSE (MANah)
3ai: ALPHA-D-MANNOSE (MANai)
3aj: ALPHA-D-MANNOSE (MANaj)
3ak: ALPHA-D-MANNOSE (MANak)
3al: ALPHA-D-MANNOSE (MANal)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
3e: ALPHA-D-MANNOSE (MANe)
3f: ALPHA-D-MANNOSE (MANf)
3g: ALPHA-D-MANNOSE (MANg)
3h: ALPHA-D-MANNOSE (MANh)
3i: ALPHA-D-MANNOSE (MANi)
3j: ALPHA-D-MANNOSE (MANj)
3k: ALPHA-D-MANNOSE (MANk)
3l: ALPHA-D-MANNOSE (MANl)
3m: ALPHA-D-MANNOSE (MANm)
3n: ALPHA-D-MANNOSE (MANn)
3o: ALPHA-D-MANNOSE (MANo)
3p: ALPHA-D-MANNOSE (MANp)
3q: ALPHA-D-MANNOSE (MANq)
3r: ALPHA-D-MANNOSE (MANr)
3s: ALPHA-D-MANNOSE (MANs)
3t: ALPHA-D-MANNOSE (MANt)
3u: ALPHA-D-MANNOSE (MANu)
3v: ALPHA-D-MANNOSE (MANv)
3w: ALPHA-D-MANNOSE (MANw)
3x: ALPHA-D-MANNOSE (MANx)
3y: ALPHA-D-MANNOSE (MANy)
3z: ALPHA-D-MANNOSE (MANz)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
5a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
5b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
5c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
5d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
5e: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDe)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
7ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
7ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
7ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
7ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
7af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
7ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7k: N-ACETYL-D-GLUCOSAMINE (NAGk)
7l: N-ACETYL-D-GLUCOSAMINE (NAGl)
7m: N-ACETYL-D-GLUCOSAMINE (NAGm)
7n: N-ACETYL-D-GLUCOSAMINE (NAGn)
7o: N-ACETYL-D-GLUCOSAMINE (NAGo)
7p: N-ACETYL-D-GLUCOSAMINE (NAGp)
7q: N-ACETYL-D-GLUCOSAMINE (NAGq)
7r: N-ACETYL-D-GLUCOSAMINE (NAGr)
7s: N-ACETYL-D-GLUCOSAMINE (NAGs)
7t: N-ACETYL-D-GLUCOSAMINE (NAGt)
7u: N-ACETYL-D-GLUCOSAMINE (NAGu)
7v: N-ACETYL-D-GLUCOSAMINE (NAGv)
7w: N-ACETYL-D-GLUCOSAMINE (NAGw)
7x: N-ACETYL-D-GLUCOSAMINE (NAGx)
7y: N-ACETYL-D-GLUCOSAMINE (NAGy)
7z: N-ACETYL-D-GLUCOSAMINE (NAGz)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
13
Ligand/Ion
BETA-D-MANNOSE
2
IFM
2
Ligand/Ion
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
3
MAN
38
Ligand/Ion
ALPHA-D-MANNOSE
4
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
MRD
5
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
6
NA
2
Ligand/Ion
SODIUM ION
7
NAG
33
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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:211 , ASN A:619
BINDING SITE FOR RESIDUE NAG A 906
02
AC2
SOFTWARE
ARG A:702 , ASN A:712 , ALA A:718 , SER A:719 , GLY A:721 , HOH A:1430
BINDING SITE FOR RESIDUE NAG A 939
03
AC3
SOFTWARE
GLU A:415 , ARG A:416 , HIS A:473 , LYS A:474 , GLY A:475 , ASN B:383 , HOH B:1338 , HOH B:1564
BINDING SITE FOR RESIDUE MRD A 940
04
AC4
SOFTWARE
ASP A:99 , SER A:357 , TRP A:358 , THR A:359 , ARG A:360 , GLU A:455 , HOH B:1147
BINDING SITE FOR RESIDUE MRD A 941
05
AC5
SOFTWARE
TRP A:68 , ARG A:98 , SER A:451 , TYR A:511 , IFM A:944 , HOH A:1141 , HOH A:1406
BINDING SITE FOR RESIDUE MPD A 942
06
AC6
SOFTWARE
ASN A:539 , NAG A:932 , HOH A:1326 , HOH A:1631
BINDING SITE FOR RESIDUE NA A 943
07
AC7
SOFTWARE
VAL A:74 , ASP A:92 , ARG A:98 , ARG A:156 , LYS A:189 , HIS A:190 , MET A:245 , TYR A:248 , ASP A:280 , TRP A:281 , SER A:451 , GLU A:509 , MPD A:942
BINDING SITE FOR RESIDUE IFM A 944
08
AC8
SOFTWARE
ASN B:211 , ASN B:619
BINDING SITE FOR RESIDUE NAG B 908
09
AC9
SOFTWARE
LYS A:414 , ASN B:658
BINDING SITE FOR RESIDUE NAG B 944
10
BC1
SOFTWARE
ARG B:702 , ASN B:712 , ALA B:718 , SER B:719
BINDING SITE FOR RESIDUE NAG B 945
11
BC2
SOFTWARE
TRP B:68 , ARG B:98 , SER B:451 , IFM B:950 , HOH B:1306 , HOH B:1440
BINDING SITE FOR RESIDUE MRD B 946
12
BC3
SOFTWARE
ASP B:99 , SER B:357 , TRP B:358 , THR B:359 , ARG B:360 , GLU B:455 , HOH B:1328
BINDING SITE FOR RESIDUE MRD B 947
13
BC4
SOFTWARE
ASN B:219 , VAL B:220 , ASN B:252 , NAG B:909
BINDING SITE FOR RESIDUE MRD B 948
14
BC5
SOFTWARE
ASN B:539 , NAG B:936 , HOH B:1686 , HOH B:1721
BINDING SITE FOR RESIDUE NA B 949
15
BC6
SOFTWARE
VAL B:74 , ASP B:92 , ARG B:98 , ARG B:156 , LYS B:189 , HIS B:190 , MET B:245 , TYR B:248 , ASP B:280 , SER B:451 , GLU B:509 , MRD B:946
BINDING SITE FOR RESIDUE IFM B 950
16
BC7
SOFTWARE
ASP A:57 , GLU A:58 , ASN A:61 , GLY A:78 , PRO A:81 , TYR A:367 , GLY A:699 , ILE A:703 , PHE A:706 , TYR A:708 , TRP A:710 , HOH A:1199 , HOH A:1382 , HOH A:1408 , HOH A:1438 , HOH A:1494 , HOH A:1507 , HOH A:1573
BINDING SITE FOR LINKED RESIDUES A 901 to 905
17
BC8
SOFTWARE
SER A:25 , PRO A:26 , VAL A:220 , ASP A:221 , ASP A:222 , ILE A:251 , ASN A:252 , TYR A:261 , THR A:262 , VAL A:827 , HOH A:1126 , HOH A:1129 , HOH A:1150 , HOH A:1277 , HOH A:1347 , HOH A:1536
BINDING SITE FOR LINKED RESIDUES A 907 to 909
18
BC9
SOFTWARE
ILE A:303 , THR A:309 , SER A:310 , PHE A:311 , ASN A:315 , SER A:720 , NAG A:913 , HOH A:1197 , HOH A:1201 , HOH A:1287 , HOH A:1356 , HOH A:1371 , HOH A:1514
BINDING SITE FOR LINKED RESIDUES A 910 to 911
19
CC1
SOFTWARE
SER A:25 , PRO A:26 , PRO A:27 , SER A:213 , ASP A:214 , GLN A:258 , HIS A:285 , SER A:286 , GLY A:287 , VAL A:288 , GLY A:289 , PHE A:311 , ASN A:315 , ILE A:318 , ASN A:322 , THR A:324 , ASP A:722 , TYR A:724 , TYR A:725 , GLY A:726 , VAL A:727 , ASP A:728 , THR A:729 , HIS A:732 , NAG A:910 , HOH A:1091 , HOH A:1103 , HOH A:1163 , HOH A:1172 , HOH A:1197 , HOH A:1228 , HOH A:1234 , HOH A:1261 , HOH A:1280 , HOH A:1291 , HOH A:1412 , HOH A:1415 , HOH A:1426 , HOH A:1476 , HOH A:1508 , HOH A:1539 , HOH A:1564 , HOH A:1577 , HOH A:1625 , HOH A:1629
BINDING SITE FOR LINKED RESIDUES A 912 to 921
20
CC2
SOFTWARE
GLU A:423 , CYS A:440 , ASN A:442 , ASP A:515 , LYS A:528 , HOH A:1092 , HOH A:1425 , HOH A:1555
BINDING SITE FOR LINKED RESIDUES A 922 to 924
21
CC3
SOFTWARE
ASP A:482 , TRP A:484 , ALA A:485 , GLN A:488 , ASP A:515 , ASN A:517 , ASN A:523 , TRP A:527 , LYS A:528 , HOH A:1041 , HOH A:1076 , HOH A:1133 , HOH A:1260 , HOH A:1469 , HOH A:1525 , HOH A:1542 , HOH A:1663 , TYR B:430 , NAG B:927 , HOH B:1464 , HOH B:1532
BINDING SITE FOR LINKED RESIDUES A 925 to 931
22
CC4
SOFTWARE
ASN A:539 , ASN A:540 , CYS A:541 , ASN A:542 , HIS A:562 , ASN A:564 , NA A:943 , HOH A:1134 , HOH A:1145 , HOH A:1236 , HOH A:1326 , HOH A:1346 , HOH A:1348 , HOH A:1389 , HOH A:1390 , HOH A:1462 , HOH A:1531 , HOH A:1608 , HOH A:1630 , THR B:359 , ASP B:361 , PHE B:365 , PHE B:368 , GLN B:371 , TYR B:375 , MAN B:943 , HOH B:1111 , HOH B:1303
BINDING SITE FOR LINKED RESIDUES A 932 to 938
23
CC5
SOFTWARE
ASP B:57 , GLU B:58 , ASN B:61 , GLY B:78 , PRO B:81 , TYR B:367 , PRO B:374 , LYS B:404 , ASN B:406 , ASP B:561 , GLY B:699 , ILE B:703 , PHE B:706 , TYR B:708 , TRP B:710 , HOH B:1136 , HOH B:1187 , HOH B:1337 , HOH B:1348 , HOH B:1356 , HOH B:1427 , HOH B:1433 , HOH B:1457 , HOH B:1459 , HOH B:1527 , HOH B:1550 , HOH B:1574 , HOH B:1604 , HOH B:1620 , HOH B:1632 , HOH B:1646 , HOH B:1658 , HOH B:1733 , HOH B:1746
BINDING SITE FOR LINKED RESIDUES B 901 to 907
24
CC6
SOFTWARE
SER B:25 , PRO B:26 , VAL B:220 , ASP B:221 , ASP B:222 , ILE B:251 , ASN B:252 , TYR B:261 , THR B:262 , VAL B:827 , ALA B:828 , GLN B:830 , MRD B:948 , HOH B:1040 , HOH B:1088 , HOH B:1263 , HOH B:1269 , HOH B:1339
BINDING SITE FOR LINKED RESIDUES B 909 to 912
25
CC7
SOFTWARE
THR B:309 , SER B:310 , PHE B:311 , ASN B:315 , SER B:719 , SER B:720 , GLY B:721 , NAG B:917 , HOH B:1045 , HOH B:1058 , HOH B:1206 , HOH B:1216 , HOH B:1405 , HOH B:1540
BINDING SITE FOR LINKED RESIDUES B 913 to 915
26
CC8
SOFTWARE
SER B:25 , PRO B:26 , PRO B:27 , SER B:213 , ASP B:214 , GLN B:258 , HIS B:285 , SER B:286 , GLY B:287 , VAL B:288 , GLY B:289 , PHE B:311 , ASN B:315 , ILE B:318 , ASN B:322 , THR B:324 , ASP B:722 , TYR B:724 , TYR B:725 , GLY B:726 , VAL B:727 , ASP B:728 , THR B:729 , HIS B:732 , PRO B:734 , NAG B:913 , HOH B:1045 , HOH B:1073 , HOH B:1089 , HOH B:1100 , HOH B:1108 , HOH B:1148 , HOH B:1185 , HOH B:1223 , HOH B:1320 , HOH B:1340 , HOH B:1379 , HOH B:1403 , HOH B:1404 , HOH B:1419 , HOH B:1465 , HOH B:1580 , HOH B:1590 , HOH B:1609 , HOH B:1610 , HOH B:1615 , HOH B:1619 , HOH B:1641 , HOH B:1661
BINDING SITE FOR LINKED RESIDUES B 916 to 925
27
CC9
SOFTWARE
MAN A:930 , GLU B:423 , CYS B:440 , ASN B:442 , ASP B:515 , LYS B:528 , HOH B:1217 , HOH B:1464 , HOH B:1520 , HOH B:1532 , HOH B:1713 , HOH B:1739
BINDING SITE FOR LINKED RESIDUES B 926 to 928
28
DC1
SOFTWARE
TYR A:430 , HOH A:1425 , ASP B:482 , TRP B:484 , ALA B:485 , GLN B:488 , ASP B:515 , ASN B:517 , ASN B:523 , TRP B:527 , LYS B:528 , HOH B:1076 , HOH B:1179 , HOH B:1261 , HOH B:1280 , HOH B:1519 , HOH B:1520 , HOH B:1714
BINDING SITE FOR LINKED RESIDUES B 929 to 935
29
DC2
SOFTWARE
THR A:359 , ASP A:361 , PHE A:368 , GLN A:371 , TYR A:375 , MAN A:938 , HOH A:1364 , ASN B:539 , ASN B:540 , ASN B:542 , HIS B:562 , ASN B:564 , NA B:949 , HOH B:1242 , HOH B:1406 , HOH B:1434 , HOH B:1509 , HOH B:1525 , HOH B:1536 , HOH B:1651 , HOH B:1719
BINDING SITE FOR LINKED RESIDUES B 936 to 943
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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