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3MVK
Asym. Unit
Info
Asym.Unit (253 KB)
Biol.Unit 1 (244 KB)
Biol.Unit 2 (54 KB)
Biol.Unit 3 (54 KB)
Biol.Unit 4 (53 KB)
Biol.Unit 5 (52 KB)
Biol.Unit 6 (53 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF FUCU FROM BIFIDOBACTERIUM LONGUM TO 1.65A
Authors
:
A. J. Stein, X. Xu, H. Cui, A. Savchenko, A. Joachimiak, Midwest Center Structural Genomics (Mcsg)
Date
:
04 May 10 (Deposition) - 12 May 10 (Release) - 12 May 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Biol. Unit 2: A,E (1x)
Biol. Unit 3: B,G (1x)
Biol. Unit 4: C,J (1x)
Biol. Unit 5: D,I (1x)
Biol. Unit 6: F,H (1x)
Keywords
:
Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. J. Stein, X. Xu, H. Cui, A. Savchenko, A. Joachimiak
The Crystal Structure Of Fucu From Bifidobacterium Longum To 1. 65A
To Be Published
[
close entry info
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Hetero Components
(4, 62)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
3h: SODIUM ION (NAh)
3i: SODIUM ION (NAi)
3j: SODIUM ION (NAj)
3k: SODIUM ION (NAk)
3l: SODIUM ION (NAl)
3m: SODIUM ION (NAm)
3n: SODIUM ION (NAn)
3o: SODIUM ION (NAo)
4a: TRIETHYLENE GLYCOL (PGEa)
4b: TRIETHYLENE GLYCOL (PGEb)
4c: TRIETHYLENE GLYCOL (PGEc)
4d: TRIETHYLENE GLYCOL (PGEd)
4e: TRIETHYLENE GLYCOL (PGEe)
4f: TRIETHYLENE GLYCOL (PGEf)
4g: TRIETHYLENE GLYCOL (PGEg)
4h: TRIETHYLENE GLYCOL (PGEh)
4i: TRIETHYLENE GLYCOL (PGEi)
4j: TRIETHYLENE GLYCOL (PGEj)
4k: TRIETHYLENE GLYCOL (PGEk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
6
Ligand/Ion
GLYCEROL
2
MSE
30
Mod. Amino Acid
SELENOMETHIONINE
3
NA
15
Ligand/Ion
SODIUM ION
4
PGE
11
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:66 , THR A:67 , GLY A:142 , VAL A:143 , HOH A:1295
BINDING SITE FOR RESIDUE NA A 149
02
AC2
SOFTWARE
ASP A:30 , PHE A:33 , ASN A:136 , GOL A:152 , HOH A:735
BINDING SITE FOR RESIDUE NA A 150
03
AC3
SOFTWARE
GLY A:23 , ASP A:24 , SER I:37 , PHE I:113
BINDING SITE FOR RESIDUE PGE A 151
04
AC4
SOFTWARE
ASP A:30 , ASN A:32 , ARG A:112 , GLN A:133 , TYR A:134 , NA A:150 , HOH A:735 , HIS G:22 , VAL G:143
BINDING SITE FOR RESIDUE GOL A 152
05
AC5
SOFTWARE
THR B:67 , GLY B:142 , VAL B:143
BINDING SITE FOR RESIDUE NA B 149
06
AC6
SOFTWARE
ASP B:30 , PHE B:33 , ASN B:136 , GOL B:152 , HOH B:1296
BINDING SITE FOR RESIDUE NA B 150
07
AC7
SOFTWARE
HIS B:22 , GLY B:23 , ASP B:24 , PHE C:113
BINDING SITE FOR RESIDUE PGE B 151
08
AC8
SOFTWARE
ASP B:30 , ASN B:32 , MSE B:76 , ARG B:112 , GLN B:133 , TYR B:134 , NA B:150 , HOH B:1296 , HIS E:22 , VAL E:143
BINDING SITE FOR RESIDUE GOL B 152
09
AC9
SOFTWARE
ASP C:66 , THR C:67 , GLY C:142 , VAL C:143 , HOH C:1013
BINDING SITE FOR RESIDUE NA C 149
10
BC1
SOFTWARE
GLY C:23 , ASP C:24 , PGE C:151 , SER F:37 , ILE F:38 , PHE F:113
BINDING SITE FOR RESIDUE PGE C 150
11
BC2
SOFTWARE
ASP C:24 , GLN C:25 , ASN C:41 , ASN C:121 , ALA C:122 , TYR C:123 , PGE C:150 , HOH C:164 , HOH C:939 , SER F:37
BINDING SITE FOR RESIDUE PGE C 151
12
BC3
SOFTWARE
ASP D:66 , THR D:67 , GLY D:142 , VAL D:143 , HOH D:1027
BINDING SITE FOR RESIDUE NA D 149
13
BC4
SOFTWARE
THR E:67 , GLY E:142 , VAL E:143 , HOH E:538
BINDING SITE FOR RESIDUE NA E 149
14
BC5
SOFTWARE
ASP E:30 , PHE E:33 , ASN E:136 , GOL E:153 , HOH E:937
BINDING SITE FOR RESIDUE NA E 150
15
BC6
SOFTWARE
GLY D:23 , ASP D:24 , SER E:37 , PHE E:113
BINDING SITE FOR RESIDUE PGE E 151
16
BC7
SOFTWARE
SER B:37 , PHE B:113 , TYR B:116 , HIS E:22 , GLY E:23 , ASP E:24 , GLN E:140
BINDING SITE FOR RESIDUE PGE E 152
17
BC8
SOFTWARE
HIS D:22 , VAL D:143 , ASP E:30 , GLN E:133 , TYR E:134 , ASN E:136 , NA E:150 , HOH E:937
BINDING SITE FOR RESIDUE GOL E 153
18
BC9
SOFTWARE
THR F:67 , GLY F:142 , VAL F:143 , HOH F:1294
BINDING SITE FOR RESIDUE NA F 149
19
CC1
SOFTWARE
ASP F:30 , PHE F:33 , ASN F:136 , GOL F:152
BINDING SITE FOR RESIDUE NA F 150
20
CC2
SOFTWARE
TYR C:68 , PHE C:145 , PRO F:80 , GLY F:81
BINDING SITE FOR RESIDUE PGE F 151
21
CC3
SOFTWARE
HIS C:22 , VAL C:143 , ASP F:30 , GLN F:133 , TYR F:134 , NA F:150
BINDING SITE FOR RESIDUE GOL F 152
22
CC4
SOFTWARE
THR G:67 , GLY G:142 , VAL G:143
BINDING SITE FOR RESIDUE NA G 149
23
CC5
SOFTWARE
SER A:37 , PHE A:113 , TYR A:116 , GLY G:23 , ASP G:24 , GLN G:140
BINDING SITE FOR RESIDUE PGE G 150
24
CC6
SOFTWARE
ASP G:30 , PHE G:33 , GLN G:133 , TYR G:134 , ASN G:136 , HIS J:22 , VAL J:143
BINDING SITE FOR RESIDUE GOL G 151
25
CC7
SOFTWARE
ASP H:66 , THR H:67 , GLY H:142 , VAL H:143 , HOH H:1135
BINDING SITE FOR RESIDUE NA H 149
26
CC8
SOFTWARE
ASP H:30 , PHE H:33 , ASN H:136 , GOL H:152 , HOH H:1297
BINDING SITE FOR RESIDUE NA H 150
27
CC9
SOFTWARE
SER H:37 , PHE H:113 , GLY I:23 , ASP I:24
BINDING SITE FOR RESIDUE PGE H 151
28
DC1
SOFTWARE
ASP H:30 , MSE H:76 , ARG H:112 , TYR H:116 , GLN H:133 , TYR H:134 , NA H:150 , HOH H:1297 , HIS I:22 , VAL I:143
BINDING SITE FOR RESIDUE GOL H 152
29
DC2
SOFTWARE
ASP I:66 , THR I:67 , GLY I:142 , VAL I:143 , HOH I:967
BINDING SITE FOR RESIDUE NA I 149
30
DC3
SOFTWARE
THR J:67 , GLY J:142 , VAL J:143 , HOH J:756
BINDING SITE FOR RESIDUE NA J 149
31
DC4
SOFTWARE
SER G:37 , GLY J:23 , ASP J:24 , GLN J:25 , ASN J:121 , ALA J:122 , TYR J:123 , PGE J:151 , HOH J:165 , HOH J:752
BINDING SITE FOR RESIDUE PGE J 150
32
DC5
SOFTWARE
ILE G:38 , PHE G:113 , GLY J:23 , ASP J:24 , PGE J:150
BINDING SITE FOR RESIDUE PGE J 151
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
View:
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Label:
End label:
Sorry, no Info available
[
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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.
SCOP Domains
(1, 10)
Info
All SCOP Domains
1a: SCOP_d3mvka_ (A:)
1b: SCOP_d3mvkb_ (B:)
1c: SCOP_d3mvkc_ (C:)
1d: SCOP_d3mvkd_ (D:)
1e: SCOP_d3mvke_ (E:)
1f: SCOP_d3mvkf_ (F:)
1g: SCOP_d3mvkg_ (G:)
1h: SCOP_d3mvkh_ (H:)
1i: SCOP_d3mvki_ (I:)
1j: SCOP_d3mvkj_ (J:)
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)
(
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(
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(
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)
(
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
RbsD-like
(12)
Superfamily
:
RbsD-like
(12)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Bifidobacterium longum [TaxId: 391904]
(1)
1a
d3mvka_
A:
1b
d3mvkb_
B:
1c
d3mvkc_
C:
1d
d3mvkd_
D:
1e
d3mvke_
E:
1f
d3mvkf_
F:
1g
d3mvkg_
G:
1h
d3mvkh_
H:
1i
d3mvki_
I:
1j
d3mvkj_
J:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
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Pfam Domains
(1, 10)
Info
all PFAM domains
1a: PFAM_RbsD_FucU_3mvkJ01 (J:5-145)
1b: PFAM_RbsD_FucU_3mvkJ02 (J:5-145)
1c: PFAM_RbsD_FucU_3mvkJ03 (J:5-145)
1d: PFAM_RbsD_FucU_3mvkJ04 (J:5-145)
1e: PFAM_RbsD_FucU_3mvkJ05 (J:5-145)
1f: PFAM_RbsD_FucU_3mvkJ06 (J:5-145)
1g: PFAM_RbsD_FucU_3mvkJ07 (J:5-145)
1h: PFAM_RbsD_FucU_3mvkJ08 (J:5-145)
1i: PFAM_RbsD_FucU_3mvkJ09 (J:5-145)
1j: PFAM_RbsD_FucU_3mvkJ10 (J:5-145)
View:
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RbsD_FucU]
(9)
Family
:
RbsD_FucU
(9)
Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12)
(1)
1a
RbsD_FucU-3mvkJ01
J:5-145
1b
RbsD_FucU-3mvkJ02
J:5-145
1c
RbsD_FucU-3mvkJ03
J:5-145
1d
RbsD_FucU-3mvkJ04
J:5-145
1e
RbsD_FucU-3mvkJ05
J:5-145
1f
RbsD_FucU-3mvkJ06
J:5-145
1g
RbsD_FucU-3mvkJ07
J:5-145
1h
RbsD_FucU-3mvkJ08
J:5-145
1i
RbsD_FucU-3mvkJ09
J:5-145
1j
RbsD_FucU-3mvkJ10
J:5-145
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