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2F2H
Asym. Unit
Info
Asym.Unit (801 KB)
Biol.Unit 1 (789 KB)
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(1)
Title
:
STRUCTURE OF THE YICI THIOSUGAR MICHAELIS COMPLEX
Authors
:
Y. -W. Kim, A. L. Lovering, N. C. J. Strynadka, S. G. Withers
Date
:
16 Nov 05 (Deposition) - 28 Feb 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Beta8Alpha8 Barrel, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. -W. Kim, A. L. Lovering, H. Chen, T. Kantner, L. P. Mcintosh, N. C. J. Strynadka, S. G. Withers
Expanding The Thioglycoligase Strategy To The Synthesis Of Alpha-Linked Thioglycosides Allows Structural Investigation Of The Parent Enzyme/Substrate Complex
J. Am. Chem. Soc. V. 128 2202 2006
[
close entry info
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Hetero Components
(4, 35)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
2a: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOa)
2b: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOb)
2c: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOc)
2d: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOd)
2e: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOe)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
4a: 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-X... (XTGa)
4b: 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-X... (XTGb)
4c: 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-X... (XTGc)
4d: 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-X... (XTGd)
4e: 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-X... (XTGe)
4f: 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-X... (XTGf)
4g: 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-X... (XTGg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
14
Ligand/Ion
GLYCEROL
2
MPO
5
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
3
SO4
9
Ligand/Ion
SULFATE ION
4
XTG
7
Ligand/Ion
4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE
[
close Hetero Component info
]
Sites
(35, 35)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR F:246 , ARG F:583 , HOH F:3246
BINDING SITE FOR RESIDUE SO4 F 3001
02
AC2
SOFTWARE
THR D:246 , ARG D:583 , HOH D:3087
BINDING SITE FOR RESIDUE SO4 D 3002
03
AC3
SOFTWARE
LYS A:403 , ARG F:677 , TYR F:680 , VAL F:681 , HOH F:3093 , HOH F:3277 , HOH F:3315
BINDING SITE FOR RESIDUE SO4 F 3003
04
AC4
SOFTWARE
THR E:246 , ARG E:583 , HOH E:3065
BINDING SITE FOR RESIDUE SO4 E 3004
05
AC5
SOFTWARE
THR C:246 , LYS C:248 , ARG C:583 , HOH C:3228
BINDING SITE FOR RESIDUE SO4 C 3005
06
AC6
SOFTWARE
THR B:246 , ARG B:583
BINDING SITE FOR RESIDUE SO4 B 3006
07
AC7
SOFTWARE
ARG F:333 , ARG F:334
BINDING SITE FOR RESIDUE SO4 F 3007
08
AC8
SOFTWARE
THR A:246 , LYS A:248 , ARG A:583 , HOH A:3191
BINDING SITE FOR RESIDUE SO4 A 3008
09
AC9
SOFTWARE
GLU E:24 , VAL E:25 , ASN E:96 , LYS E:114
BINDING SITE FOR RESIDUE SO4 E 3009
10
BC1
SOFTWARE
HIS B:640 , ASP B:642 , GLN B:653 , HIS B:654 , GLY B:655 , SER B:658 , HOH B:3282
BINDING SITE FOR RESIDUE MPO B 3010
11
BC2
SOFTWARE
HIS C:640 , ASP C:642 , GLN C:653 , HIS C:654 , GLY C:655 , SER C:658 , HOH C:3347
BINDING SITE FOR RESIDUE MPO C 3011
12
BC3
SOFTWARE
HIS D:640 , ASP D:642 , GLN D:652 , GLN D:653 , HIS D:654 , GLY D:655 , SER D:658 , HOH D:3325
BINDING SITE FOR RESIDUE MPO D 3012
13
BC4
SOFTWARE
HOH D:3303 , HIS E:640 , GLN E:652 , GLN E:653 , HIS E:654 , GLY E:655 , SER E:658
BINDING SITE FOR RESIDUE MPO E 3013
14
BC5
SOFTWARE
HIS F:640 , GLN F:653 , HIS F:654 , GLY F:655 , SER F:658 , HOH F:3153
BINDING SITE FOR RESIDUE MPO F 3014
15
BC6
SOFTWARE
ASP A:185 , PHE A:277 , THR A:278 , ASP A:306 , CYS A:307 , TRP A:380 , LYS A:414 , ASP A:416 , ARG A:466 , TRP A:479 , ASP A:482 , PHE A:515 , HIS A:540 , SER A:542 , HOH A:3030 , HOH A:3033 , HOH A:3118 , HOH A:3157 , THR B:45 , LEU B:48 , ASP B:49
BINDING SITE FOR RESIDUE XTG A 3015
16
BC7
SOFTWARE
ASP B:185 , ASP B:306 , TRP B:380 , LYS B:414 , ASP B:416 , ARG B:466 , TRP B:479 , ASP B:482 , PHE B:515 , HIS B:540 , SER B:542 , HOH B:3035 , HOH B:3068 , TRP C:8 , LEU F:48 , ASP F:49 , HOH F:3224
BINDING SITE FOR RESIDUE XTG B 3016
17
BC8
SOFTWARE
ASP C:185 , PHE C:277 , THR C:278 , ASP C:306 , CYS C:307 , TRP C:380 , LYS C:414 , ASP C:416 , PHE C:417 , ARG C:466 , TRP C:479 , ASP C:482 , PHE C:515 , HIS C:540 , SER C:542 , LYS C:543 , HOH C:3049 , HOH C:3085 , HOH C:3189 , HOH C:3273 , THR D:45 , ASP D:49
BINDING SITE FOR RESIDUE XTG C 3017
18
BC9
SOFTWARE
ASP D:185 , ASP D:306 , LYS D:414 , ASP D:416 , ARG D:420 , ARG D:466 , TRP D:479 , ASP D:482 , PHE D:515 , ARG D:538 , HIS D:540 , LYS D:543 , HOH D:3167 , HOH D:3284 , THR E:45 , ASP E:49 , HOH E:3117
BINDING SITE FOR RESIDUE XTG D 3018
19
CC1
SOFTWARE
ASP C:49 , ASP E:185 , PHE E:277 , THR E:278 , ASP E:306 , TRP E:380 , ASP E:416 , PHE E:417 , ARG E:466 , TRP E:479 , ASP E:482 , PHE E:515 , HIS E:540 , SER E:542 , LYS E:543 , HOH E:3120 , HOH E:3153 , HOH E:3273 , TRP F:8
BINDING SITE FOR RESIDUE XTG E 3019
20
CC2
SOFTWARE
LEU A:48 , ASP A:49 , ASP F:185 , PHE F:277 , ASP F:306 , TRP F:380 , LYS F:414 , ASP F:416 , ARG F:466 , TRP F:479 , ASP F:482 , PHE F:515 , HIS F:540 , LYS F:543 , HOH F:3038 , HOH F:3052 , HOH F:3149 , HOH F:3234
BINDING SITE FOR RESIDUE XTG F 3020
21
CC3
SOFTWARE
GLU A:329 , TRP F:267 , HIS F:301 , LYS F:336 , ALA F:337 , GLY F:339 , LEU F:340 , ARG F:677 , PRO F:678 , ASP F:679 , HOH F:3047 , HOH F:3062
BINDING SITE FOR RESIDUE XTG F 3021
22
CC4
SOFTWARE
THR A:455 , VAL A:456 , PRO F:265 , ALA F:266 , TRP F:267 , GLU F:460 , TYR F:574 , ASP F:679 , HOH F:3273 , HOH F:3274
BINDING SITE FOR RESIDUE GOL F 3022
23
CC5
SOFTWARE
ARG C:68 , ASN C:211 , GLU C:238 , GOL C:3030 , HOH C:3081 , HOH C:3218 , HOH C:3365
BINDING SITE FOR RESIDUE GOL C 3023
24
CC6
SOFTWARE
GLN A:27 , ASP A:29 , VAL A:92 , THR A:93 , ILE A:94 , HOH A:3308
BINDING SITE FOR RESIDUE GOL A 3024
25
CC7
SOFTWARE
GLU B:31 , PHE B:58 , ARG B:68 , GLU B:238 , GOL B:3026
BINDING SITE FOR RESIDUE GOL B 3025
26
CC8
SOFTWARE
ARG B:68 , HIS B:81 , ASN B:211 , GLU B:238 , GOL B:3025 , HOH B:3238 , HOH B:3285
BINDING SITE FOR RESIDUE GOL B 3026
27
CC9
SOFTWARE
TRP B:8 , ASP C:482 , TYR C:484 , PHE C:515 , HOH C:3266
BINDING SITE FOR RESIDUE GOL C 3027
28
DC1
SOFTWARE
GLU A:31 , PHE A:58 , ARG A:68 , GLU A:238 , GOL A:3029 , HOH A:3342
BINDING SITE FOR RESIDUE GOL A 3028
29
DC2
SOFTWARE
ARG A:68 , HIS A:81 , ASN A:211 , GLU A:238 , GOL A:3028 , HOH A:3127 , HOH A:3137 , HOH A:3333
BINDING SITE FOR RESIDUE GOL A 3029
30
DC3
SOFTWARE
GLU C:31 , PHE C:58 , ARG C:68 , GLU C:238 , GOL C:3023 , HOH C:3365
BINDING SITE FOR RESIDUE GOL C 3030
31
DC4
SOFTWARE
GLU D:31 , PHE D:58 , ARG D:68 , GLU D:238 , HOH D:3318 , HOH D:3322
BINDING SITE FOR RESIDUE GOL D 3031
32
DC5
SOFTWARE
ARG D:68 , HIS D:81 , LEU D:84 , ASN D:211 , GLU D:238 , HOH D:3098 , HOH D:3145 , HOH D:3209
BINDING SITE FOR RESIDUE GOL D 3032
33
DC6
SOFTWARE
GLU E:31 , PHE E:58 , ARG E:68 , GLU E:238 , HOH E:3191
BINDING SITE FOR RESIDUE GOL E 3033
34
DC7
SOFTWARE
GLU F:31 , PHE F:58 , ARG F:68 , GLU F:238
BINDING SITE FOR RESIDUE GOL F 3034
35
DC8
SOFTWARE
ASP E:482 , TYR E:484 , PHE E:515 , GLU E:516 , TRP F:8
BINDING SITE FOR RESIDUE GOL E 3035
[
close Site info
]
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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.
SCOP Domains
(4, 24)
Info
All SCOP Domains
1a: SCOP_d2f2ha3 (A:586-665)
1b: SCOP_d2f2hb3 (B:586-665)
1c: SCOP_d2f2hc3 (C:586-665)
1d: SCOP_d2f2hd3 (D:586-665)
1e: SCOP_d2f2he3 (E:586-665)
1f: SCOP_d2f2hf3 (F:586-665)
2a: SCOP_d2f2ha1 (A:666-773)
2b: SCOP_d2f2hb1 (B:666-773)
2c: SCOP_d2f2hc1 (C:666-773)
2d: SCOP_d2f2hd1 (D:666-773)
2e: SCOP_d2f2he1 (E:666-773)
2f: SCOP_d2f2hf1 (F:666-773)
3a: SCOP_d2f2ha2 (A:1-247)
3b: SCOP_d2f2hb2 (B:1-247)
3c: SCOP_d2f2hc2 (C:1-247)
3d: SCOP_d2f2hd2 (D:1-247)
3e: SCOP_d2f2he2 (E:1-247)
3f: SCOP_d2f2hf2 (F:1-247)
4a: SCOP_d2f2ha4 (A:248-585)
4b: SCOP_d2f2hb4 (B:248-585)
4c: SCOP_d2f2hc4 (C:248-585)
4d: SCOP_d2f2hd4 (D:248-585)
4e: SCOP_d2f2he4 (E:248-585)
4f: SCOP_d2f2hf4 (F:248-585)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
Families
(
)
(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
Putative glucosidase YicI, domain 3
(5)
Protein domain
:
Putative glucosidase YicI, domain 3
(5)
Escherichia coli [TaxId: 562]
(5)
1a
d2f2ha3
A:586-665
1b
d2f2hb3
B:586-665
1c
d2f2hc3
C:586-665
1d
d2f2hd3
D:586-665
1e
d2f2he3
E:586-665
1f
d2f2hf3
F:586-665
Fold
:
Putative glucosidase YicI, C-terminal domain
(5)
Superfamily
:
Putative glucosidase YicI, C-terminal domain
(5)
Family
:
Putative glucosidase YicI, C-terminal domain
(5)
Protein domain
:
Putative glucosidase YicI, C-terminal domain
(5)
Escherichia coli [TaxId: 562]
(5)
2a
d2f2ha1
A:666-773
2b
d2f2hb1
B:666-773
2c
d2f2hc1
C:666-773
2d
d2f2hd1
D:666-773
2e
d2f2he1
E:666-773
2f
d2f2hf1
F:666-773
Fold
:
Supersandwich
(271)
Superfamily
:
Galactose mutarotase-like
(205)
Family
:
YicI N-terminal domain-like
(6)
Protein domain
:
Putative glucosidase YicI, N-terminal domain
(5)
Escherichia coli [TaxId: 562]
(5)
3a
d2f2ha2
A:1-247
3b
d2f2hb2
B:1-247
3c
d2f2hc2
C:1-247
3d
d2f2hd2
D:1-247
3e
d2f2he2
E:1-247
3f
d2f2hf2
F:1-247
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
YicI catalytic domain-like
(6)
Protein domain
:
Putative glucosidase YicI, domain 2
(5)
Escherichia coli [TaxId: 562]
(5)
4a
d2f2ha4
A:248-585
4b
d2f2hb4
B:248-585
4c
d2f2hc4
C:248-585
4d
d2f2hd4
D:248-585
4e
d2f2he4
E:248-585
4f
d2f2hf4
F:248-585
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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