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1WPB
Biol. Unit 3
Info
Asym.Unit (500 KB)
Biol.Unit 1 (732 KB)
Biol.Unit 2 (730 KB)
Biol.Unit 3 (126 KB)
Biol.Unit 4 (127 KB)
Biol.Unit 5 (127 KB)
Biol.Unit 6 (128 KB)
Biol.Unit 7 (126 KB)
Biol.Unit 8 (127 KB)
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(1)
Title
:
STRUCTURE OF ESCHERICHIA COLI YFBU GENE PRODUCT
Authors
:
D. Borek, Y. Chen, M. Zheng, T. Skarina, A. Savchenko, A. Edwards, Z. Otw Midwest Center For Structural Genomics (Mcsg)
Date
:
01 Sep 04 (Deposition) - 07 Dec 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,G,H (3x)
Biol. Unit 2: I,J,K,L,M,N,O,P (3x)
Biol. Unit 3: B,C,F,G (1x)
Biol. Unit 4: J,K,N,O (1x)
Biol. Unit 5: I,L,M,P (1x)
Biol. Unit 6: A,D,E,H (1x)
Biol. Unit 7: B,C,F,G (1x)
Biol. Unit 8: J,K,N,O (1x)
Keywords
:
Structural Genomics, Mcsg, Ncs, Regulatory Protein, Protein Structure Initiative, Psi, Midwest Center For Structural Genomics, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Borek, Y. Chen, M. Zheng, T. Skarina, A. Savchenko, A. Edwards, Z. Otwinowski
Crystal Structure Of Escherichia Coli Yfbu Gene Product
To Be Published
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1aa: CHLORIDE ION (CLaa)
1ab: CHLORIDE ION (CLab)
1ac: CHLORIDE ION (CLac)
1ad: CHLORIDE ION (CLad)
1ae: CHLORIDE ION (CLae)
1af: CHLORIDE ION (CLaf)
1ag: CHLORIDE ION (CLag)
1ah: CHLORIDE ION (CLah)
1ai: CHLORIDE ION (CLai)
1aj: CHLORIDE ION (CLaj)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
1l: CHLORIDE ION (CLl)
1m: CHLORIDE ION (CLm)
1n: CHLORIDE ION (CLn)
1o: CHLORIDE ION (CLo)
1p: CHLORIDE ION (CLp)
1q: CHLORIDE ION (CLq)
1r: CHLORIDE ION (CLr)
1s: CHLORIDE ION (CLs)
1t: CHLORIDE ION (CLt)
1u: CHLORIDE ION (CLu)
1v: CHLORIDE ION (CLv)
1w: CHLORIDE ION (CLw)
1x: CHLORIDE ION (CLx)
1y: CHLORIDE ION (CLy)
1z: CHLORIDE ION (CLz)
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)
2ar: GLYCEROL (GOLar)
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
CL
-1
Ligand/Ion
CHLORIDE ION
2
GOL
4
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC6 (SOFTWARE)
03: BC1 (SOFTWARE)
04: CC1 (SOFTWARE)
05: CC3 (SOFTWARE)
06: DC2 (SOFTWARE)
07: DC4 (SOFTWARE)
08: DC5 (SOFTWARE)
09: DC6 (SOFTWARE)
10: DC7 (SOFTWARE)
11: DC8 (SOFTWARE)
12: DC9 (SOFTWARE)
13: EC2 (SOFTWARE)
14: FC3 (SOFTWARE)
15: FC5 (SOFTWARE)
16: FC7 (SOFTWARE)
17: FC8 (SOFTWARE)
18: FC9 (SOFTWARE)
19: GC1 (SOFTWARE)
20: GC2 (SOFTWARE)
21: GC3 (SOFTWARE)
22: HC5 (SOFTWARE)
23: HC6 (SOFTWARE)
24: HC8 (SOFTWARE)
25: HC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
GLN B:20 , GLN C:20 , GLN F:20 , GLN G:20
BINDING SITE FOR RESIDUE CL C 2004
02
AC6
SOFTWARE
GLN B:13 , GLN C:13 , GLN F:13 , GLN G:13
BINDING SITE FOR RESIDUE CL C 2006
03
BC1
SOFTWARE
HIS B:76
BINDING SITE FOR RESIDUE CL B 2010
04
CC1
SOFTWARE
HIS C:79
BINDING SITE FOR RESIDUE CL C 2021
05
CC3
SOFTWARE
HIS F:79 , VAL F:80
BINDING SITE FOR RESIDUE CL F 2023
06
DC2
SOFTWARE
SER C:160 , ASN C:162
BINDING SITE FOR RESIDUE CL C 2031
07
DC4
SOFTWARE
HIS G:79
BINDING SITE FOR RESIDUE CL G 2033
08
DC5
SOFTWARE
HIS F:76
BINDING SITE FOR RESIDUE CL F 2034
09
DC6
SOFTWARE
GLU F:59 , LYS F:61 , THR F:64 , ARG F:108
BINDING SITE FOR RESIDUE CL F 2035
10
DC7
SOFTWARE
GLU B:120 , GLN G:49 , GLU G:52 , HIS G:151 , GLN G:156 , HOH G:3091
BINDING SITE FOR RESIDUE GOL G 3001
11
DC8
SOFTWARE
ARG C:37 , GLN C:49 , GLU C:52 , HIS E:151 , GLN E:156 , HOH E:3047 , MET F:116 , GLU F:120
BINDING SITE FOR RESIDUE GOL E 3002
12
DC9
SOFTWARE
ARG B:37 , GLN B:49 , GLU B:52 , HOH B:3104 , GLU C:120 , HIS D:151 , GLN D:156
BINDING SITE FOR RESIDUE GOL B 3003
13
EC2
SOFTWARE
ARG D:37 , GLN D:49 , GLU D:52 , MET E:116 , GLU E:120 , HIS F:151 , GLN F:156 , HOH F:3085
BINDING SITE FOR RESIDUE GOL D 3005
14
FC3
SOFTWARE
HIS B:151 , GLN B:156 , ARG F:37 , GLN F:49 , GLU F:52 , MET G:116 , GLU G:120
BINDING SITE FOR RESIDUE GOL B 3015
15
FC5
SOFTWARE
ARG B:66 , HOH B:3109 , ARG G:66 , THR G:67 , ASP G:70 , HOH G:3070 , HOH G:3101 , HOH G:3126
BINDING SITE FOR RESIDUE GOL B 3017
16
FC7
SOFTWARE
ARG C:66 , THR C:67 , ASP C:70 , HOH C:3064 , ARG D:66 , HOH D:3129
BINDING SITE FOR RESIDUE GOL D 3019
17
FC8
SOFTWARE
HIS C:76 , ARG C:122 , TYR C:123 , HOH C:3098 , HOH C:3135 , HIS D:76 , HOH D:3075 , HOH D:3104
BINDING SITE FOR RESIDUE GOL D 3020
18
FC9
SOFTWARE
ARG B:55 , ARG C:66 , HOH C:3113 , HOH C:3120 , THR D:67 , ASP D:70
BINDING SITE FOR RESIDUE GOL C 3021
19
GC1
SOFTWARE
GLY E:121 , ARG E:122 , TYR E:123 , THR E:124 , HOH E:3064 , HOH E:3122 , TYR F:157 , HIS F:158
BINDING SITE FOR RESIDUE GOL E 3022
20
GC2
SOFTWARE
GLY B:121 , ARG B:122 , TYR B:123 , THR B:124 , HOH B:3118 , HIS G:76 , HOH G:3086
BINDING SITE FOR RESIDUE GOL B 3023
21
GC3
SOFTWARE
THR B:67 , ASP B:70 , LEU B:147 , HOH B:3093 , HOH B:3113 , ARG G:66
BINDING SITE FOR RESIDUE GOL B 3024
22
HC5
SOFTWARE
ARG D:51 , GLU D:52 , ARG E:66 , THR F:67 , ASP F:70 , HIS F:151
BINDING SITE FOR RESIDUE GOL E 3035
23
HC6
SOFTWARE
LEU A:48 , GLN A:49 , GLU A:52 , ASP C:70 , HIS C:151 , GLN C:156 , HOH C:3053 , GLU D:120
BINDING SITE FOR RESIDUE GOL C 3036
24
HC8
SOFTWARE
HIS B:76 , ARG G:122 , TYR G:123 , HOH G:3078 , HOH G:3122
BINDING SITE FOR RESIDUE GOL G 3038
25
HC9
SOFTWARE
GLU E:73 , HIS E:76 , TYR E:157 , ARG F:122 , TYR F:123 , HOH F:3048 , HOH F:3088
BINDING SITE FOR RESIDUE GOL F 3039
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 16)
Info
All SCOP Domains
1a: SCOP_d1wpba_ (A:)
1b: SCOP_d1wpbb_ (B:)
1c: SCOP_d1wpbk_ (K:)
1d: SCOP_d1wpbl_ (L:)
1e: SCOP_d1wpbm_ (M:)
1f: SCOP_d1wpbn_ (N:)
1g: SCOP_d1wpbo_ (O:)
1h: SCOP_d1wpbp_ (P:)
1i: SCOP_d1wpbc_ (C:)
1j: SCOP_d1wpbd_ (D:)
1k: SCOP_d1wpbe_ (E:)
1l: SCOP_d1wpbf_ (F:)
1m: SCOP_d1wpbg_ (G:)
1n: SCOP_d1wpbh_ (H:)
1o: SCOP_d1wpbi_ (I:)
1p: SCOP_d1wpbj_ (J:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
YfbU-like
(1)
Superfamily
:
YfbU-like
(1)
Family
:
YfbU-like
(1)
Protein domain
:
Hypothetical protein YfbU
(1)
Escherichia coli [TaxId: 562]
(1)
1a
d1wpba_
A:
1b
d1wpbb_
B:
1c
d1wpbk_
K:
1d
d1wpbl_
L:
1e
d1wpbm_
M:
1f
d1wpbn_
N:
1g
d1wpbo_
O:
1h
d1wpbp_
P:
1i
d1wpbc_
C:
1j
d1wpbd_
D:
1k
d1wpbe_
E:
1l
d1wpbf_
F:
1m
d1wpbg_
G:
1n
d1wpbh_
H:
1o
d1wpbi_
I:
1p
d1wpbj_
J:
[
close SCOP info
]
CATH Domains
(2, 32)
Info
all CATH domains
1a: CATH_1wpbM01 (M:4-58)
1b: CATH_1wpbO01 (O:3-57)
1c: CATH_1wpbL01 (L:3-58)
1d: CATH_1wpbN01 (N:3-58)
1e: CATH_1wpbP01 (P:3-58)
1f: CATH_1wpbA01 (A:3-60)
1g: CATH_1wpbD01 (D:3-48)
1h: CATH_1wpbI01 (I:3-48)
1i: CATH_1wpbG01 (G:3-56)
1j: CATH_1wpbB01 (B:3-58)
1k: CATH_1wpbC01 (C:3-58)
1l: CATH_1wpbE01 (E:3-58)
1m: CATH_1wpbF01 (F:3-58)
1n: CATH_1wpbH01 (H:3-58)
1o: CATH_1wpbJ01 (J:3-58)
1p: CATH_1wpbK01 (K:3-58)
2a: CATH_1wpbO02 (O:58-170)
2b: CATH_1wpbG02 (G:57-170)
2c: CATH_1wpbM02 (M:59-170)
2d: CATH_1wpbN02 (N:59-170)
2e: CATH_1wpbP02 (P:59-170)
2f: CATH_1wpbA02 (A:61-170)
2g: CATH_1wpbD02 (D:49-170)
2h: CATH_1wpbI02 (I:49-170)
2i: CATH_1wpbB02 (B:59-170)
2j: CATH_1wpbC02 (C:59-170)
2k: CATH_1wpbE02 (E:59-170)
2l: CATH_1wpbF02 (F:59-170)
2m: CATH_1wpbH02 (H:59-170)
2n: CATH_1wpbJ02 (J:59-170)
2o: CATH_1wpbK02 (K:59-170)
2p: CATH_1wpbL02 (L:59-170)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(1)
Escherichia coli. Organism_taxid: 562.
(1)
1a
1wpbM01
M:4-58
1b
1wpbO01
O:3-57
1c
1wpbL01
L:3-58
1d
1wpbN01
N:3-58
1e
1wpbP01
P:3-58
1f
1wpbA01
A:3-60
1g
1wpbD01
D:3-48
1h
1wpbI01
I:3-48
1i
1wpbG01
G:3-56
1j
1wpbB01
B:3-58
1k
1wpbC01
C:3-58
1l
1wpbE01
E:3-58
1m
1wpbF01
F:3-58
1n
1wpbH01
H:3-58
1o
1wpbJ01
J:3-58
1p
1wpbK01
K:3-58
Topology
:
yfbu gene product, domain 2
(1)
Homologous Superfamily
:
yfbu gene product, domain 2
(1)
Escherichia coli. Organism_taxid: 562.
(1)
2a
1wpbO02
O:58-170
2b
1wpbG02
G:57-170
2c
1wpbM02
M:59-170
2d
1wpbN02
N:59-170
2e
1wpbP02
P:59-170
2f
1wpbA02
A:61-170
2g
1wpbD02
D:49-170
2h
1wpbI02
I:49-170
2i
1wpbB02
B:59-170
2j
1wpbC02
C:59-170
2k
1wpbE02
E:59-170
2l
1wpbF02
F:59-170
2m
1wpbH02
H:59-170
2n
1wpbJ02
J:59-170
2o
1wpbK02
K:59-170
2p
1wpbL02
L:59-170
[
close CATH info
]
Pfam Domains
(1, 16)
Info
all PFAM domains
1a: PFAM_YfbU_1wpbP01 (P:7-170)
1b: PFAM_YfbU_1wpbP02 (P:7-170)
1c: PFAM_YfbU_1wpbP03 (P:7-170)
1d: PFAM_YfbU_1wpbP04 (P:7-170)
1e: PFAM_YfbU_1wpbP05 (P:7-170)
1f: PFAM_YfbU_1wpbP06 (P:7-170)
1g: PFAM_YfbU_1wpbP07 (P:7-170)
1h: PFAM_YfbU_1wpbP08 (P:7-170)
1i: PFAM_YfbU_1wpbP09 (P:7-170)
1j: PFAM_YfbU_1wpbP10 (P:7-170)
1k: PFAM_YfbU_1wpbP11 (P:7-170)
1l: PFAM_YfbU_1wpbP12 (P:7-170)
1m: PFAM_YfbU_1wpbP13 (P:7-170)
1n: PFAM_YfbU_1wpbP14 (P:7-170)
1o: PFAM_YfbU_1wpbP15 (P:7-170)
1p: PFAM_YfbU_1wpbP16 (P:7-170)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: YfbU]
(1)
Family
:
YfbU
(1)
Escherichia coli (strain UTI89 / UPEC)
(1)
1a
YfbU-1wpbP01
P:7-170
1b
YfbU-1wpbP02
P:7-170
1c
YfbU-1wpbP03
P:7-170
1d
YfbU-1wpbP04
P:7-170
1e
YfbU-1wpbP05
P:7-170
1f
YfbU-1wpbP06
P:7-170
1g
YfbU-1wpbP07
P:7-170
1h
YfbU-1wpbP08
P:7-170
1i
YfbU-1wpbP09
P:7-170
1j
YfbU-1wpbP10
P:7-170
1k
YfbU-1wpbP11
P:7-170
1l
YfbU-1wpbP12
P:7-170
1m
YfbU-1wpbP13
P:7-170
1n
YfbU-1wpbP14
P:7-170
1o
YfbU-1wpbP15
P:7-170
1p
YfbU-1wpbP16
P:7-170
[
close Pfam info
]
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select residue range 5 to 10 in chain 'A'
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (500 KB)
Header - Asym.Unit
Biol.Unit 1 (732 KB)
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Biol.Unit 3 (126 KB)
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Biol.Unit 5 (127 KB)
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(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
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