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1WPB
Biol. Unit 6
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, 7)
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
7
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC8 (SOFTWARE)
03: BC2 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC9 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC4 (SOFTWARE)
08: DC3 (SOFTWARE)
09: DC8 (SOFTWARE)
10: DC9 (SOFTWARE)
11: EC1 (SOFTWARE)
12: EC2 (SOFTWARE)
13: EC3 (SOFTWARE)
14: FC4 (SOFTWARE)
15: FC6 (SOFTWARE)
16: FC7 (SOFTWARE)
17: FC8 (SOFTWARE)
18: FC9 (SOFTWARE)
19: GC1 (SOFTWARE)
20: GC4 (SOFTWARE)
21: HC5 (SOFTWARE)
22: HC6 (SOFTWARE)
23: HC7 (SOFTWARE)
24: HC9 (SOFTWARE)
25: IC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
GLN A:20 , GLN D:20 , GLN E:20 , GLN H:20
BINDING SITE FOR RESIDUE CL H 2005
02
AC8
SOFTWARE
GLN A:13 , GLN D:13 , GLN E:13 , GLN H:13
BINDING SITE FOR RESIDUE CL D 2008
03
BC2
SOFTWARE
HIS D:76
BINDING SITE FOR RESIDUE CL D 2012
04
BC3
SOFTWARE
HIS H:76
BINDING SITE FOR RESIDUE CL H 2014
05
BC9
SOFTWARE
HIS A:79
BINDING SITE FOR RESIDUE CL A 2020
06
CC2
SOFTWARE
HIS D:79 , VAL D:80
BINDING SITE FOR RESIDUE CL D 2022
07
CC4
SOFTWARE
VAL H:80
BINDING SITE FOR RESIDUE CL H 2024
08
DC3
SOFTWARE
HIS E:79
BINDING SITE FOR RESIDUE CL E 2032
09
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
10
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
11
EC1
SOFTWARE
HIS A:151 , GLN A:156 , HOH A:3082 , ARG E:37 , GLN E:49 , GLU E:52 , GLU H:120
BINDING SITE FOR RESIDUE GOL E 3004
12
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
13
EC3
SOFTWARE
MET A:116 , GLU A:120 , ARG H:37 , GLN H:49 , GLU H:52 , HIS H:151 , GLN H:156 , HOH H:3035
BINDING SITE FOR RESIDUE GOL H 3006
14
FC4
SOFTWARE
ARG A:66 , ARG H:51 , THR H:67 , ASP H:70 , HIS H:151 , HOH H:3091 , HOH H:3095
BINDING SITE FOR RESIDUE GOL H 3016
15
FC6
SOFTWARE
ARG D:122 , TYR D:123 , THR D:124 , HIS D:125 , HOH D:3128
BINDING SITE FOR RESIDUE GOL D 3018
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
GC4
SOFTWARE
THR A:67 , ASP A:70 , HOH A:3119 , HOH E:3078 , ARG H:66 , HOH H:3041
BINDING SITE FOR RESIDUE GOL H 3025
21
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
22
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
23
HC7
SOFTWARE
GLU A:73 , HIS A:76 , TYR A:157 , ARG H:122 , TYR H:123 , HOH H:3066
BINDING SITE FOR RESIDUE GOL A 3037
24
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
25
IC1
SOFTWARE
ARG A:122 , TYR A:123 , HOH A:3058 , HOH A:3073 , HOH A:3090 , GLU H:73 , HIS H:76 , TYR H:157
BINDING SITE FOR RESIDUE GOL A 3040
[
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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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (500 KB)
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Biol.Unit 1 (732 KB)
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Biol.Unit 3 (126 KB)
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