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2DCN
Biol. Unit 2
Info
Asym.Unit (646 KB)
Biol.Unit 1 (321 KB)
Biol.Unit 2 (324 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 2-KETO-3-DEOXYGLUCONATE KINASE FROM SULFOLOBUS TOKODAII COMPLEXED WITH 2-KETO-6-PHOSPHOGLUCONATE (ALPHA-FURANOSE FORM)
Authors
:
S. Okazaki, H. Onda, A. Suzuki, S. Kuramitsu, R. Masui, T. Yamane
Date
:
10 Jan 06 (Deposition) - 31 Jan 06 (Release) - 24 May 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
2-Keto-3-Deoxygluconate Kinase, Sulfolobus Tokodaii, 2-Keto-D- Gluconate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Okazaki, H. Onda, A. Suzuki, S. Kuramitsu, R. Masui, T. Yamane
Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed With 2-Keto-6-Phosphogluconat
To Be Published
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
1h: ADENOSINE-5'-DIPHOSPHATE (ADPh)
1i: ADENOSINE-5'-DIPHOSPHATE (ADPi)
1j: ADENOSINE-5'-DIPHOSPHATE (ADPj)
1k: ADENOSINE-5'-DIPHOSPHATE (ADPk)
1l: ADENOSINE-5'-DIPHOSPHATE (ADPl)
2a: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPa)
2b: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPb)
2c: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPc)
2d: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPd)
2e: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPe)
2f: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPf)
2g: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPg)
2h: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPh)
2i: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPi)
2j: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPj)
2k: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPk)
2l: (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[... (CKPl)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
3e: POTASSIUM ION (Ke)
3f: POTASSIUM ION (Kf)
3g: POTASSIUM ION (Kg)
3h: POTASSIUM ION (Kh)
3i: POTASSIUM ION (Ki)
3j: POTASSIUM ION (Kj)
3k: POTASSIUM ION (Kk)
3l: POTASSIUM ION (Kl)
4a: MAGNESIUM ION (MGa)
4aa: MAGNESIUM ION (MGaa)
4ab: MAGNESIUM ION (MGab)
4ac: MAGNESIUM ION (MGac)
4ad: MAGNESIUM ION (MGad)
4ae: MAGNESIUM ION (MGae)
4af: MAGNESIUM ION (MGaf)
4ag: MAGNESIUM ION (MGag)
4ah: MAGNESIUM ION (MGah)
4ai: MAGNESIUM ION (MGai)
4aj: MAGNESIUM ION (MGaj)
4ak: MAGNESIUM ION (MGak)
4al: MAGNESIUM ION (MGal)
4am: MAGNESIUM ION (MGam)
4an: MAGNESIUM ION (MGan)
4ao: MAGNESIUM ION (MGao)
4ap: MAGNESIUM ION (MGap)
4aq: MAGNESIUM ION (MGaq)
4ar: MAGNESIUM ION (MGar)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
4k: MAGNESIUM ION (MGk)
4l: MAGNESIUM ION (MGl)
4m: MAGNESIUM ION (MGm)
4n: MAGNESIUM ION (MGn)
4o: MAGNESIUM ION (MGo)
4p: MAGNESIUM ION (MGp)
4q: MAGNESIUM ION (MGq)
4r: MAGNESIUM ION (MGr)
4s: MAGNESIUM ION (MGs)
4t: MAGNESIUM ION (MGt)
4u: MAGNESIUM ION (MGu)
4v: MAGNESIUM ION (MGv)
4w: MAGNESIUM ION (MGw)
4x: MAGNESIUM ION (MGx)
4y: MAGNESIUM ION (MGy)
4z: MAGNESIUM ION (MGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
6
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CKP
6
Ligand/Ion
(2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[(PHOSPHONATOOXY)METHYL]TETRAHYDROFURAN-2-CARBOXYLIC ACID
3
K
-1
Ligand/Ion
POTASSIUM ION
4
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(33, 33)
Info
All Sites
01: BC9 (SOFTWARE)
02: CC1 (SOFTWARE)
03: CC2 (SOFTWARE)
04: CC3 (SOFTWARE)
05: CC4 (SOFTWARE)
06: CC5 (SOFTWARE)
07: CC6 (SOFTWARE)
08: CC7 (SOFTWARE)
09: CC8 (SOFTWARE)
10: CC9 (SOFTWARE)
11: DC1 (SOFTWARE)
12: DC2 (SOFTWARE)
13: DC3 (SOFTWARE)
14: DC4 (SOFTWARE)
15: DC5 (SOFTWARE)
16: EC3 (SOFTWARE)
17: EC4 (SOFTWARE)
18: EC5 (SOFTWARE)
19: EC6 (SOFTWARE)
20: EC7 (SOFTWARE)
21: EC8 (SOFTWARE)
22: FC6 (SOFTWARE)
23: FC7 (SOFTWARE)
24: FC8 (SOFTWARE)
25: FC9 (SOFTWARE)
26: GC1 (SOFTWARE)
27: GC2 (SOFTWARE)
28: GC9 (SOFTWARE)
29: HC1 (SOFTWARE)
30: HC2 (SOFTWARE)
31: HC3 (SOFTWARE)
32: HC4 (SOFTWARE)
33: HC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC9
SOFTWARE
ASN G:164 , CKP G:2007 , ADP G:3007 , HOH G:5128 , HOH G:5133 , HOH G:5134
BINDING SITE FOR RESIDUE MG G 4022
02
CC1
SOFTWARE
ADP G:3007 , HOH G:5123
BINDING SITE FOR RESIDUE MG G 4023
03
CC2
SOFTWARE
TYR G:125
BINDING SITE FOR RESIDUE MG G 4026
04
CC3
SOFTWARE
ASN H:164 , CKP H:2008 , ADP H:3008 , HOH H:5179 , HOH H:5180 , HOH H:5181
BINDING SITE FOR RESIDUE MG H 4029
05
CC4
SOFTWARE
ADP H:3008 , HOH H:5172
BINDING SITE FOR RESIDUE MG H 4030
06
CC5
SOFTWARE
ASN I:164 , CKP I:2009 , ADP I:3009 , HOH I:5176 , HOH I:5177 , HOH I:5178
BINDING SITE FOR RESIDUE MG I 4031
07
CC6
SOFTWARE
ADP I:3009 , HOH I:5064 , HOH I:5114 , HOH I:5183
BINDING SITE FOR RESIDUE MG I 4032
08
CC7
SOFTWARE
VAL I:76
BINDING SITE FOR RESIDUE MG I 4033
09
CC8
SOFTWARE
ASN J:164 , CKP J:2010 , ADP J:3010 , HOH J:5094 , HOH J:5174 , HOH J:5175
BINDING SITE FOR RESIDUE MG J 4034
10
CC9
SOFTWARE
ADP J:3010 , HOH J:5086
BINDING SITE FOR RESIDUE MG J 4035
11
DC1
SOFTWARE
TYR J:125
BINDING SITE FOR RESIDUE MG J 4037
12
DC2
SOFTWARE
ASN K:164 , CKP K:2011 , ADP K:3011 , HOH K:5127 , HOH K:5128 , HOH K:5129
BINDING SITE FOR RESIDUE MG K 4038
13
DC3
SOFTWARE
ADP K:3011 , HOH K:5063
BINDING SITE FOR RESIDUE MG K 4039
14
DC4
SOFTWARE
ASN L:164 , CKP L:2012 , ADP L:3012 , HOH L:5169 , HOH L:5170 , HOH L:5171
BINDING SITE FOR RESIDUE MG L 4042
15
DC5
SOFTWARE
ADP L:3012 , HOH L:5158
BINDING SITE FOR RESIDUE MG L 4043
16
EC3
SOFTWARE
ASP G:250 , THR G:252 , ASN G:286 , ILE G:289 , GLY G:291 , HOH G:5016
BINDING SITE FOR RESIDUE K G 5007
17
EC4
SOFTWARE
ASP H:250 , THR H:252 , ASN H:286 , ILE H:289 , GLY H:291 , HOH H:5044
BINDING SITE FOR RESIDUE K H 5008
18
EC5
SOFTWARE
ASP I:250 , THR I:252 , ASN I:286 , ILE I:289 , GLY I:291 , HOH I:5047
BINDING SITE FOR RESIDUE K I 5009
19
EC6
SOFTWARE
ASP J:250 , THR J:252 , ASN J:286 , ILE J:289 , GLY J:291 , HOH J:5021
BINDING SITE FOR RESIDUE K J 5010
20
EC7
SOFTWARE
ASP K:250 , THR K:252 , ASN K:286 , ILE K:289 , GLY K:291 , HOH K:5024
BINDING SITE FOR RESIDUE K K 5011
21
EC8
SOFTWARE
ASP L:250 , THR L:252 , ASN L:286 , ILE L:289 , GLY L:291 , HOH L:5061
BINDING SITE FOR RESIDUE K L 5012
22
FC6
SOFTWARE
LEU G:11 , ALA G:33 , GLY G:34 , SER G:35 , PHE G:90 , TYR G:106 , ARG G:108 , ILE G:137 , ASN G:164 , ARG G:166 , GLY G:253 , ALA G:254 , ASP G:256 , ASP G:292 , ADP G:3007 , MG G:4022 , HOH G:5040 , HOH G:5084 , HOH G:5133 , HOH G:5136
BINDING SITE FOR RESIDUE CKP G 2007
23
FC7
SOFTWARE
LEU H:11 , ALA H:33 , GLY H:34 , SER H:35 , PHE H:90 , TYR H:106 , ARG H:108 , ILE H:137 , ASN H:164 , ARG H:166 , GLY H:253 , GLY H:255 , ASP H:256 , ASP H:292 , ADP H:3008 , MG H:4029 , HOH H:5180 , HOH H:5183
BINDING SITE FOR RESIDUE CKP H 2008
24
FC8
SOFTWARE
LEU I:11 , ALA I:33 , GLY I:34 , SER I:35 , PHE I:90 , TYR I:106 , ARG I:108 , ASN I:164 , ARG I:166 , THR I:252 , GLY I:253 , ALA I:254 , GLY I:255 , ASP I:256 , ASP I:292 , ADP I:3009 , MG I:4031 , HOH I:5022 , HOH I:5038 , HOH I:5180
BINDING SITE FOR RESIDUE CKP I 2009
25
FC9
SOFTWARE
LEU J:11 , ALA J:33 , GLY J:34 , SER J:35 , PHE J:90 , TYR J:106 , ARG J:108 , ILE J:137 , ASN J:164 , ARG J:166 , GLY J:253 , ALA J:254 , GLY J:255 , ASP J:256 , ASP J:292 , ADP J:3010 , MG J:4034 , HOH J:5019 , HOH J:5033 , HOH J:5174 , HOH J:5177
BINDING SITE FOR RESIDUE CKP J 2010
26
GC1
SOFTWARE
LEU K:11 , ALA K:33 , GLY K:34 , SER K:35 , PHE K:90 , TYR K:106 , ARG K:108 , ILE K:137 , ASN K:164 , ARG K:166 , GLY K:253 , ASP K:256 , ASP K:292 , ADP K:3011 , MG K:4038 , HOH K:5056 , HOH K:5077 , HOH K:5131
BINDING SITE FOR RESIDUE CKP K 2011
27
GC2
SOFTWARE
LEU L:11 , ALA L:33 , GLY L:34 , SER L:35 , PHE L:90 , TYR L:106 , ARG L:108 , ILE L:137 , ASN L:164 , ARG L:166 , GLY L:253 , ASP L:256 , ASP L:292 , ADP L:3012 , MG L:4042 , HOH L:5013 , HOH L:5023 , HOH L:5169 , HOH L:5173
BINDING SITE FOR RESIDUE CKP L 2012
28
GC9
SOFTWARE
ASP G:194 , LYS G:224 , GLY G:226 , PRO G:227 , GLY G:229 , TYR G:244 , VAL G:248 , VAL G:251 , ALA G:254 , GLY G:255 , LEU G:258 , ILE G:280 , SER G:283 , VAL G:287 , CKP G:2007 , MG G:4022 , MG G:4023 , HOH G:5019 , HOH G:5029 , HOH G:5031 , HOH G:5060 , HOH G:5076 , HOH G:5122 , HOH G:5123
BINDING SITE FOR RESIDUE ADP G 3007
29
HC1
SOFTWARE
ASP H:194 , LYS H:224 , GLY H:226 , GLY H:229 , TYR H:244 , VAL H:248 , ALA H:254 , GLY H:255 , LEU H:258 , SER H:283 , VAL H:287 , CKP H:2008 , MG H:4029 , MG H:4030 , HOH H:5010 , HOH H:5022 , HOH H:5093 , HOH H:5180 , HOH H:5183
BINDING SITE FOR RESIDUE ADP H 3008
30
HC2
SOFTWARE
ASP I:194 , LYS I:224 , GLY I:226 , PRO I:227 , GLY I:229 , TYR I:244 , VAL I:248 , ALA I:254 , GLY I:255 , SER I:283 , VAL I:287 , CKP I:2009 , MG I:4031 , MG I:4032 , HOH I:5029 , HOH I:5043 , HOH I:5064 , HOH I:5075 , HOH I:5114 , HOH I:5136 , HOH I:5143 , HOH I:5183
BINDING SITE FOR RESIDUE ADP I 3009
31
HC3
SOFTWARE
ASP J:194 , LYS J:224 , GLY J:226 , PRO J:227 , GLY J:229 , TYR J:244 , VAL J:248 , VAL J:251 , ALA J:254 , GLY J:255 , SER J:283 , VAL J:287 , CKP J:2010 , MG J:4034 , MG J:4035 , HOH J:5016 , HOH J:5027 , HOH J:5043 , HOH J:5048 , HOH J:5086 , HOH J:5117 , HOH J:5132 , HOH J:5178
BINDING SITE FOR RESIDUE ADP J 3010
32
HC4
SOFTWARE
ASP K:194 , LYS K:224 , GLY K:226 , PRO K:227 , GLY K:229 , TYR K:244 , VAL K:248 , VAL K:251 , ALA K:254 , GLY K:255 , SER K:283 , VAL K:287 , CKP K:2011 , MG K:4038 , MG K:4039 , HOH K:5012 , HOH K:5038 , HOH K:5070 , HOH K:5083 , HOH K:5108 , HOH K:5131
BINDING SITE FOR RESIDUE ADP K 3011
33
HC5
SOFTWARE
ASP L:194 , LYS L:224 , GLY L:226 , PRO L:227 , GLY L:229 , TYR L:244 , VAL L:248 , VAL L:251 , ALA L:254 , GLY L:255 , ILE L:280 , SER L:283 , CKP L:2012 , MG L:4042 , MG L:4043 , HOH L:5030 , HOH L:5032 , HOH L:5036 , HOH L:5045 , HOH L:5064 , HOH L:5129 , HOH L:5170 , HOH L:5173
BINDING SITE FOR RESIDUE ADP L 3012
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Sorry, no Info available
[
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Exons
(0, 0)
Info
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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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2dcnb_ (B:)
1b: SCOP_d2dcnc_ (C:)
1c: SCOP_d2dcnl_ (L:)
1d: SCOP_d2dcnd_ (D:)
1e: SCOP_d2dcne_ (E:)
1f: SCOP_d2dcnf_ (F:)
1g: SCOP_d2dcng_ (G:)
1h: SCOP_d2dcnh_ (H:)
1i: SCOP_d2dcni_ (I:)
1j: SCOP_d2dcnj_ (J:)
1k: SCOP_d2dcnk_ (K:)
2a: SCOP_d2dcna1 (A:2-309)
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Protein Domains
(
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(
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribokinase-like
(226)
Superfamily
:
Ribokinase-like
(189)
Family
:
automated matches
(88)
Protein domain
:
automated matches
(88)
Sulfolobus tokodaii [TaxId: 273063]
(2)
1a
d2dcnb_
B:
1b
d2dcnc_
C:
1c
d2dcnl_
L:
1d
d2dcnd_
D:
1e
d2dcne_
E:
1f
d2dcnf_
F:
1g
d2dcng_
G:
1h
d2dcnh_
H:
1i
d2dcni_
I:
1j
d2dcnj_
J:
1k
d2dcnk_
K:
Family
:
Ribokinase-like
(36)
Protein domain
:
Hypothetical fructokinase ST2478
(1)
Sulfolobus tokodaii [TaxId: 111955]
(1)
2a
d2dcna1
A:2-309
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
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Sorry, no Info available
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