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1GQO
Biol. Unit 1
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Asym.Unit (591 KB)
Biol.Unit 1 (297 KB)
Biol.Unit 2 (295 KB)
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(1)
Title
:
TYPE II DEHYDROQUINASE FROM BACILLUS SUBTILIS
Authors
:
D. A. Robinson, A. W. Roszak, J. R. Coggins, A. J. Lapthorn
Date
:
28 Nov 01 (Deposition) - 12 Dec 02 (Release) - 07 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,X,Y
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Biol. Unit 2: M,N,O,P,Q,R,S,T,U,V,X,Y (1x)
Keywords
:
Dehydratase, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. A. Robinson, A. W. Roszak, J. R. Coggins, A. J. Lapthorn
Crystal Structure Of The Type Ii Dehydroquinase From Bacillus Subtilis
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 36)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1aa: GLYCEROL (GOLaa)
1ab: GLYCEROL (GOLab)
1ac: GLYCEROL (GOLac)
1ad: GLYCEROL (GOLad)
1ae: GLYCEROL (GOLae)
1af: GLYCEROL (GOLaf)
1ag: GLYCEROL (GOLag)
1ah: GLYCEROL (GOLah)
1ai: GLYCEROL (GOLai)
1aj: GLYCEROL (GOLaj)
1ak: GLYCEROL (GOLak)
1al: GLYCEROL (GOLal)
1am: GLYCEROL (GOLam)
1an: GLYCEROL (GOLan)
1ao: GLYCEROL (GOLao)
1ap: GLYCEROL (GOLap)
1aq: GLYCEROL (GOLaq)
1ar: GLYCEROL (GOLar)
1as: GLYCEROL (GOLas)
1at: GLYCEROL (GOLat)
1au: GLYCEROL (GOLau)
1av: GLYCEROL (GOLav)
1aw: GLYCEROL (GOLaw)
1ax: GLYCEROL (GOLax)
1ay: GLYCEROL (GOLay)
1az: GLYCEROL (GOLaz)
1b: GLYCEROL (GOLb)
1ba: GLYCEROL (GOLba)
1bb: GLYCEROL (GOLbb)
1bc: GLYCEROL (GOLbc)
1bd: GLYCEROL (GOLbd)
1be: GLYCEROL (GOLbe)
1bf: GLYCEROL (GOLbf)
1bg: GLYCEROL (GOLbg)
1bh: GLYCEROL (GOLbh)
1bi: GLYCEROL (GOLbi)
1bj: GLYCEROL (GOLbj)
1bk: GLYCEROL (GOLbk)
1bl: GLYCEROL (GOLbl)
1bm: GLYCEROL (GOLbm)
1bn: GLYCEROL (GOLbn)
1bo: GLYCEROL (GOLbo)
1bp: GLYCEROL (GOLbp)
1bq: GLYCEROL (GOLbq)
1br: GLYCEROL (GOLbr)
1bs: GLYCEROL (GOLbs)
1bt: GLYCEROL (GOLbt)
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)
1o: GLYCEROL (GOLo)
1p: GLYCEROL (GOLp)
1q: GLYCEROL (GOLq)
1r: GLYCEROL (GOLr)
1s: GLYCEROL (GOLs)
1t: GLYCEROL (GOLt)
1u: GLYCEROL (GOLu)
1v: GLYCEROL (GOLv)
1w: GLYCEROL (GOLw)
1x: GLYCEROL (GOLx)
1y: GLYCEROL (GOLy)
1z: GLYCEROL (GOLz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
36
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(36, 36)
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)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:79 , LEU A:103 , ARG A:106 , ARG A:110 , GOL A:152 , ASP B:86
BINDING SITE FOR RESIDUE GOL A 150
02
AC2
SOFTWARE
GLN A:112 , SER A:113 , HOH A:2088 , HOH A:2089 , TYR D:104 , HIS D:111 , HOH D:2077
BINDING SITE FOR RESIDUE GOL A 151
03
AC3
SOFTWARE
ASN A:10 , ARG A:13 , LEU A:14 , ARG A:17 , PHE A:22 , GOL A:150
BINDING SITE FOR RESIDUE GOL A 152
04
AC4
SOFTWARE
PHE B:22 , GLY B:75 , HIS B:79 , HIS B:99 , ARG B:106 , ARG B:110 , HOH C:2055
BINDING SITE FOR RESIDUE GOL B 150
05
AC5
SOFTWARE
GLN B:112 , SER B:113 , PRO B:117 , HOH B:2096 , HOH B:2097 , HOH B:2098 , TYR G:104 , HIS G:111 , HOH G:2071
BINDING SITE FOR RESIDUE GOL B 151
06
AC6
SOFTWARE
ASN B:10 , ARG B:13 , LEU B:14 , ARG B:17 , PHE B:22
BINDING SITE FOR RESIDUE GOL B 152
07
AC7
SOFTWARE
ASP A:86 , GLY C:75 , HIS C:79 , HIS C:99 , LEU C:103 , ARG C:106 , ARG C:110
BINDING SITE FOR RESIDUE GOL C 150
08
AC8
SOFTWARE
GLN C:112 , SER C:113 , VAL C:114 , PRO C:117 , HOH C:2097 , HOH C:2098 , TYR J:104 , HIS J:111 , HOH J:2071
BINDING SITE FOR RESIDUE GOL C 151
09
AC9
SOFTWARE
ASN C:10 , ARG C:13 , LEU C:14 , ARG C:17 , PHE C:22 , HOH C:2009 , HOH C:2099 , HOH C:2100
BINDING SITE FOR RESIDUE GOL C 152
10
BC1
SOFTWARE
PHE D:22 , GLY D:75 , HIS D:79 , HIS D:99 , LEU D:103 , ARG D:106 , ARG D:110 , GOL D:152 , ASP E:86
BINDING SITE FOR RESIDUE GOL D 150
11
BC2
SOFTWARE
HIS A:111 , GLN D:112 , SER D:113 , PRO D:117 , HOH D:2052 , HOH D:2094 , HOH D:2095
BINDING SITE FOR RESIDUE GOL D 151
12
BC3
SOFTWARE
ASN D:10 , LEU D:14 , ARG D:17 , PHE D:22 , GOL D:150 , HOH D:2096
BINDING SITE FOR RESIDUE GOL D 152
13
BC4
SOFTWARE
GLY E:75 , HIS E:79 , LEU E:103 , ARG E:106 , ARG E:110 , GOL E:152 , ASP F:86
BINDING SITE FOR RESIDUE GOL E 150
14
BC5
SOFTWARE
GLN E:112 , SER E:113 , PRO E:117 , HOH E:2091 , HOH E:2092 , HOH E:2093 , TYR L:104 , HIS L:111 , HOH L:2070
BINDING SITE FOR RESIDUE GOL E 151
15
BC6
SOFTWARE
ASN E:10 , LEU E:14 , ARG E:17 , PHE E:22 , GOL E:150
BINDING SITE FOR RESIDUE GOL E 152
16
BC7
SOFTWARE
GLY F:75 , HIS F:79 , HIS F:99 , LEU F:103 , ARG F:106 , ARG F:110 , HOH F:2086 , HOH F:2088
BINDING SITE FOR RESIDUE GOL F 150
17
BC8
SOFTWARE
GLN F:112 , SER F:113 , VAL F:114 , HOH F:2046 , HOH F:2090 , HOH F:2091 , TYR H:104 , HIS H:111
BINDING SITE FOR RESIDUE GOL F 151
18
BC9
SOFTWARE
ASN F:10 , LEU F:14 , ARG F:17 , PHE F:22
BINDING SITE FOR RESIDUE GOL F 152
19
CC1
SOFTWARE
PHE G:22 , GLY G:75 , HIS G:79 , HIS G:99 , LEU G:103 , ARG G:106 , ARG G:110 , GOL G:152 , HOH G:2089
BINDING SITE FOR RESIDUE GOL G 150
20
CC2
SOFTWARE
TYR B:104 , HIS B:111 , HOH B:2075 , GLN G:112 , SER G:113 , HOH G:2090 , HOH G:2091
BINDING SITE FOR RESIDUE GOL G 151
21
CC3
SOFTWARE
ASN G:10 , LEU G:14 , ARG G:17 , PHE G:22 , GOL G:150 , HOH G:2002
BINDING SITE FOR RESIDUE GOL G 152
22
CC4
SOFTWARE
PHE H:22 , ASN H:73 , GLY H:75 , ALA H:76 , HIS H:79 , HIS H:99 , LEU H:103 , ARG H:106 , ARG H:110 , GOL H:152 , HOH H:2039
BINDING SITE FOR RESIDUE GOL H 150
23
CC5
SOFTWARE
TYR F:104 , HIS F:111 , HOH F:2067 , GLN H:112 , SER H:113 , PRO H:117 , HOH H:2074 , HOH H:2075
BINDING SITE FOR RESIDUE GOL H 151
24
CC6
SOFTWARE
ASN H:10 , ARG H:13 , ARG H:17 , PHE H:22 , GOL H:150 , HOH H:2001
BINDING SITE FOR RESIDUE GOL H 152
25
CC7
SOFTWARE
GLY I:75 , ALA I:76 , HIS I:79 , HIS I:99 , ARG I:106 , ARG I:110 , HOH I:2087
BINDING SITE FOR RESIDUE GOL I 150
26
CC8
SOFTWARE
GLN I:112 , SER I:113 , PRO I:117 , HOH I:2088 , HOH I:2090 , TYR K:104 , HIS K:111
BINDING SITE FOR RESIDUE GOL I 151
27
CC9
SOFTWARE
ASN I:10 , ARG I:13 , LEU I:14 , ARG I:17 , PHE I:22 , HOH I:2091
BINDING SITE FOR RESIDUE GOL I 152
28
DC1
SOFTWARE
PHE J:22 , GLY J:75 , HIS J:79 , HIS J:99 , LEU J:103 , ARG J:106 , ARG J:110 , HOH J:2088 , HOH J:2089 , ASP K:86 , HOH K:2043
BINDING SITE FOR RESIDUE GOL J 150
29
DC2
SOFTWARE
TYR C:104 , HIS C:111 , HOH C:2077 , GLN J:112 , SER J:113 , PRO J:117 , HOH J:2090 , HOH J:2091
BINDING SITE FOR RESIDUE GOL J 151
30
DC3
SOFTWARE
ASN J:10 , ARG J:13 , LEU J:14 , PHE J:22 , HOH J:2003 , HOH K:2043
BINDING SITE FOR RESIDUE GOL J 152
31
DC4
SOFTWARE
HIS K:79 , HIS K:99 , LEU K:103 , ARG K:106 , ARG K:110 , GOL K:152
BINDING SITE FOR RESIDUE GOL K 150
32
DC5
SOFTWARE
TYR I:104 , HIS I:111 , GLN K:112 , SER K:113 , PRO K:117 , HOH K:2079 , HOH K:2080
BINDING SITE FOR RESIDUE GOL K 151
33
DC6
SOFTWARE
ASN K:10 , ARG K:13 , LEU K:14 , ARG K:17 , GOL K:150 , HOH K:2081 , HOH K:2082 , HOH K:2083
BINDING SITE FOR RESIDUE GOL K 152
34
DC7
SOFTWARE
HIS L:79 , HIS L:99 , LEU L:103 , ARG L:106 , ARG L:110 , GOL L:152 , HOH L:2056
BINDING SITE FOR RESIDUE GOL L 150
35
DC8
SOFTWARE
TYR E:104 , HIS E:111 , HOH E:2072 , GLN L:112 , SER L:113 , VAL L:114 , PRO L:117 , HOH L:2084 , HOH L:2085
BINDING SITE FOR RESIDUE GOL L 151
36
DC9
SOFTWARE
ASN L:10 , LEU L:14 , GOL L:150 , HOH L:2003 , HOH L:2060 , HOH L:2086
BINDING SITE FOR RESIDUE GOL L 152
[
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
(1, 12)
Info
All PROSITE Patterns/Profiles
1: DEHYDROQUINASE_II (A:6-23,B:6-23,C:6-23,D:6-23,E:6-23...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DEHYDROQUINASE_II
PS01029
Dehydroquinase class II signature.
AROQ_BACSU
7-24
12
A:6-23
B:6-23
C:6-23
D:6-23
E:6-23
F:6-23
G:6-23
H:6-23
I:6-23
J:6-23
K:6-23
L:6-23
-
-
-
-
-
-
-
-
-
-
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 24)
Info
All SCOP Domains
1a: SCOP_d1gqoa_ (A:)
1b: SCOP_d1gqob_ (B:)
1c: SCOP_d1gqok_ (K:)
1d: SCOP_d1gqol_ (L:)
1e: SCOP_d1gqom_ (M:)
1f: SCOP_d1gqon_ (N:)
1g: SCOP_d1gqoo_ (O:)
1h: SCOP_d1gqop_ (P:)
1i: SCOP_d1gqoq_ (Q:)
1j: SCOP_d1gqor_ (R:)
1k: SCOP_d1gqos_ (S:)
1l: SCOP_d1gqot_ (T:)
1m: SCOP_d1gqoc_ (C:)
1n: SCOP_d1gqou_ (U:)
1o: SCOP_d1gqov_ (V:)
1p: SCOP_d1gqox_ (X:)
1q: SCOP_d1gqoy_ (Y:)
1r: SCOP_d1gqod_ (D:)
1s: SCOP_d1gqoe_ (E:)
1t: SCOP_d1gqof_ (F:)
1u: SCOP_d1gqog_ (G:)
1v: SCOP_d1gqoh_ (H:)
1w: SCOP_d1gqoi_ (I:)
1x: SCOP_d1gqoj_ (J:)
View:
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)
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)
Folds
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)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Type II 3-dehydroquinate dehydratase
(40)
Family
:
Type II 3-dehydroquinate dehydratase
(38)
Protein domain
:
Type II 3-dehydroquinate dehydratase
(20)
Bacillus subtilis [TaxId: 1423]
(1)
1a
d1gqoa_
A:
1b
d1gqob_
B:
1c
d1gqok_
K:
1d
d1gqol_
L:
1e
d1gqom_
M:
1f
d1gqon_
N:
1g
d1gqoo_
O:
1h
d1gqop_
P:
1i
d1gqoq_
Q:
1j
d1gqor_
R:
1k
d1gqos_
S:
1l
d1gqot_
T:
1m
d1gqoc_
C:
1n
d1gqou_
U:
1o
d1gqov_
V:
1p
d1gqox_
X:
1q
d1gqoy_
Y:
1r
d1gqod_
D:
1s
d1gqoe_
E:
1t
d1gqof_
F:
1u
d1gqog_
G:
1v
d1gqoh_
H:
1w
d1gqoi_
I:
1x
d1gqoj_
J:
[
close SCOP info
]
CATH Domains
(1, 24)
Info
all CATH domains
1a: CATH_1gqoB00 (B:1-143)
1b: CATH_1gqoA00 (A:1-141)
1c: CATH_1gqoL00 (L:1-141)
1d: CATH_1gqoM00 (M:1-141)
1e: CATH_1gqoO00 (O:1-141)
1f: CATH_1gqoP00 (P:1-141)
1g: CATH_1gqoQ00 (Q:1-141)
1h: CATH_1gqoR00 (R:1-141)
1i: CATH_1gqoS00 (S:1-141)
1j: CATH_1gqoT00 (T:1-141)
1k: CATH_1gqoU00 (U:1-141)
1l: CATH_1gqoY00 (Y:1-141)
1m: CATH_1gqoC00 (C:1-141)
1n: CATH_1gqoK00 (K:1-141)
1o: CATH_1gqoV00 (V:1-141)
1p: CATH_1gqoX00 (X:1-141)
1q: CATH_1gqoN00 (N:1-141)
1r: CATH_1gqoD00 (D:1-141)
1s: CATH_1gqoE00 (E:1-141)
1t: CATH_1gqoF00 (F:1-141)
1u: CATH_1gqoG00 (G:1-141)
1v: CATH_1gqoH00 (H:1-141)
1w: CATH_1gqoI00 (I:1-141)
1x: CATH_1gqoJ00 (J:1-141)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.9100, no name defined]
(22)
Bacillus subtilis. Organism_taxid: 1423.
(1)
1a
1gqoB00
B:1-143
1b
1gqoA00
A:1-141
1c
1gqoL00
L:1-141
1d
1gqoM00
M:1-141
1e
1gqoO00
O:1-141
1f
1gqoP00
P:1-141
1g
1gqoQ00
Q:1-141
1h
1gqoR00
R:1-141
1i
1gqoS00
S:1-141
1j
1gqoT00
T:1-141
1k
1gqoU00
U:1-141
1l
1gqoY00
Y:1-141
1m
1gqoC00
C:1-141
1n
1gqoK00
K:1-141
1o
1gqoV00
V:1-141
1p
1gqoX00
X:1-141
1q
1gqoN00
N:1-141
1r
1gqoD00
D:1-141
1s
1gqoE00
E:1-141
1t
1gqoF00
F:1-141
1u
1gqoG00
G:1-141
1v
1gqoH00
H:1-141
1w
1gqoI00
I:1-141
1x
1gqoJ00
J:1-141
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
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