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1WUU
Biol. Unit 1
Info
Asym.Unit (263 KB)
Biol.Unit 1 (128 KB)
Biol.Unit 2 (130 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN GALACTOKINASE COMPLEXED WITH MGAMPPNP AND GALACTOSE
Authors
:
J. B. Thoden, D. J. Timson, R. J. Reece, H. M. Holden
Date
:
08 Dec 04 (Deposition) - 28 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Galactosemia, Ghmp Superfamily, Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. B. Thoden, D. J. Timson, R. J. Reece, H. M. Holden
Molecular Structure Of Human Galactokinase: Implications For Type Ii Galactosemia
J. Biol. Chem. V. 280 9662 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 20)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
1c: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPc)
1d: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPd)
2a: ALPHA D-GALACTOSE (GLAa)
2b: ALPHA D-GALACTOSE (GLAb)
2c: ALPHA D-GALACTOSE (GLAc)
2d: ALPHA D-GALACTOSE (GLAd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: SELENOMETHIONINE (MSEa)
4aa: SELENOMETHIONINE (MSEaa)
4ab: SELENOMETHIONINE (MSEab)
4ac: SELENOMETHIONINE (MSEac)
4ad: SELENOMETHIONINE (MSEad)
4ae: SELENOMETHIONINE (MSEae)
4af: SELENOMETHIONINE (MSEaf)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
4y: SELENOMETHIONINE (MSEy)
4z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
2
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
GLA
2
Ligand/Ion
ALPHA D-GALACTOSE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
MSE
16
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:37 , GLU A:43 , HIS A:44 , ASP A:46 , TYR A:47 , CYS A:182 , GLY A:183 , MSE A:185 , ASP A:186 , TYR A:236 , GLY A:346 , MG A:394 , ANP A:395 , HOH A:442 , HOH A:483
BINDING SITE FOR RESIDUE GLA A 393
2
AC2
SOFTWARE
ARG B:37 , GLU B:43 , HIS B:44 , ASP B:46 , TYR B:47 , CYS B:182 , GLY B:183 , MSE B:185 , ASP B:186 , TYR B:236 , GLY B:346 , ANP B:395 , HOH B:444 , HOH B:446
BINDING SITE FOR RESIDUE GLA B 393
3
AC5
SOFTWARE
SER A:140 , SER A:142 , GLA A:393 , ANP A:395
BINDING SITE FOR RESIDUE MG A 394
4
AC6
SOFTWARE
SER B:142 , ASP B:186 , ANP B:395
BINDING SITE FOR RESIDUE MG B 394
5
AC9
SOFTWARE
ARG A:37 , THR A:77 , SER A:79 , TRP A:106 , TYR A:109 , SER A:131 , LEU A:135 , GLY A:136 , GLY A:137 , GLY A:138 , LEU A:139 , SER A:140 , SER A:141 , SER A:142 , LEU A:145 , ARG A:228 , GLY A:345 , GLY A:346 , GLA A:393 , MG A:394 , HOH A:434 , HOH A:438 , HOH A:446
BINDING SITE FOR RESIDUE ANP A 395
6
BC1
SOFTWARE
ARG B:37 , THR B:77 , TRP B:106 , TYR B:109 , VAL B:129 , PRO B:134 , LEU B:135 , GLY B:136 , GLY B:137 , GLY B:138 , LEU B:139 , SER B:140 , SER B:141 , SER B:142 , ARG B:228 , GLY B:345 , GLY B:346 , GLA B:393 , MG B:394 , HOH B:442
BINDING SITE FOR RESIDUE ANP B 395
[
close Site info
]
SAPs(SNPs)/Variants
(14, 28)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_008514 (P28T, chain A/B, )
02: VAR_002547 (V32M, chain A/B, )
03: VAR_023486 (G36R, chain A/B, )
04: VAR_023487 (H44Y, chain A/B, )
05: VAR_023488 (R68C, chain A/B, )
06: VAR_023489 (I184M, chain A/B, )
07: VAR_015746 (A198V, chain A/B, )
08: VAR_023490 (R239Q, chain A/B, )
09: VAR_023491 (G274D, chain A/B, )
10: VAR_023492 (T288M, chain A/B, )
11: VAR_023493 (V338A, chain A/B, )
12: VAR_023494 (G346S, chain A/B, )
13: VAR_023495 (G349S, chain A/B, )
14: VAR_023496 (A384P, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_008514
P
28
T
GALK1_HUMAN
Disease (GALCT2)
---
A/B
P
28
T
02
UniProt
VAR_002547
V
32
M
GALK1_HUMAN
Disease (GALCT2)
---
A/B
V
32
M
03
UniProt
VAR_023486
G
36
R
GALK1_HUMAN
Disease (GALCT2)
---
A/B
G
36
R
04
UniProt
VAR_023487
H
44
Y
GALK1_HUMAN
Disease (GALCT2)
---
A/B
H
44
Y
05
UniProt
VAR_023488
R
68
C
GALK1_HUMAN
Disease (GALCT2)
---
A/B
R
68
C
06
UniProt
VAR_023489
I
184
M
GALK1_HUMAN
Polymorphism
---
A/B
I
184
M
07
UniProt
VAR_015746
A
198
V
GALK1_HUMAN
Disease (GALCT2)
80084721
A/B
A
198
V
08
UniProt
VAR_023490
R
239
Q
GALK1_HUMAN
Disease (GALCT2)
---
A/B
R
239
Q
09
UniProt
VAR_023491
G
274
D
GALK1_HUMAN
Polymorphism
---
A/B
G
274
D
10
UniProt
VAR_023492
T
288
M
GALK1_HUMAN
Disease (GALCT2)
---
A/B
T
288
M
11
UniProt
VAR_023493
V
338
A
GALK1_HUMAN
Polymorphism
---
A/B
V
338
A
12
UniProt
VAR_023494
G
346
S
GALK1_HUMAN
Disease (GALCT2)
---
A/B
G
346
S
13
UniProt
VAR_023495
G
349
S
GALK1_HUMAN
Disease (GALCT2)
---
A/B
G
349
S
14
UniProt
VAR_023496
A
384
P
GALK1_HUMAN
Disease (GALCT2)
---
A/B
A
384
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: GALACTOKINASE (A:36-47,B:36-47)
2: GHMP_KINASES_ATP (A:133-144,B:133-144)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GALACTOKINASE
PS00106
Galactokinase signature.
GALK1_HUMAN
36-47
2
A:36-47
B:36-47
-
-
2
GHMP_KINASES_ATP
PS00627
GHMP kinases putative ATP-binding domain.
GALK1_HUMAN
133-144
2
A:133-144
B:133-144
-
-
[
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]
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1wuua2 (A:217-392)
1b: SCOP_d1wuub2 (B:217-392)
1c: SCOP_d1wuuc2 (C:217-392)
1d: SCOP_d1wuud2 (D:217-392)
2a: SCOP_d1wuua1 (A:2-216)
2b: SCOP_d1wuub1 (B:2-216)
2c: SCOP_d1wuuc1 (C:2-216)
2d: SCOP_d1wuud1 (D:2-216)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
GHMP Kinase, C-terminal domain
(25)
Family
:
Galactokinase
(3)
Protein domain
:
Galactokinase
(3)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1wuua2
A:217-392
1b
d1wuub2
B:217-392
1c
d1wuuc2
C:217-392
1d
d1wuud2
D:217-392
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
GHMP Kinase, N-terminal domain
(19)
Protein domain
:
Galactokinase
(3)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1wuua1
A:2-216
2b
d1wuub1
B:2-216
2c
d1wuuc1
C:2-216
2d
d1wuud1
D:2-216
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1wuuA02 (A:213-382)
1b: CATH_1wuuC02 (C:213-382)
1c: CATH_1wuuD02 (D:213-382)
1d: CATH_1wuuB02 (B:213-382)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.890, no name defined]
(18)
Human (Homo sapiens)
(2)
1a
1wuuA02
A:213-382
1b
1wuuC02
C:213-382
1c
1wuuD02
D:213-382
1d
1wuuB02
B:213-382
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_GHMP_kinases_N_1wuuD01 (D:126-194)
1b: PFAM_GHMP_kinases_N_1wuuD02 (D:126-194)
1c: PFAM_GHMP_kinases_N_1wuuD03 (D:126-194)
1d: PFAM_GHMP_kinases_N_1wuuD04 (D:126-194)
2a: PFAM_GHMP_kinases_C_1wuuD05 (D:291-374)
2b: PFAM_GHMP_kinases_C_1wuuD06 (D:291-374)
2c: PFAM_GHMP_kinases_C_1wuuD07 (D:291-374)
2d: PFAM_GHMP_kinases_C_1wuuD08 (D:291-374)
3a: PFAM_GalKase_gal_bdg_1wuuD09 (D:17-68)
3b: PFAM_GalKase_gal_bdg_1wuuD10 (D:17-68)
3c: PFAM_GalKase_gal_bdg_1wuuD11 (D:17-68)
3d: PFAM_GalKase_gal_bdg_1wuuD12 (D:17-68)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
S5
(103)
Family
:
GHMP_kinases_N
(23)
Homo sapiens (Human)
(2)
1a
GHMP_kinases_N-1wuuD01
D:126-194
1b
GHMP_kinases_N-1wuuD02
D:126-194
1c
GHMP_kinases_N-1wuuD03
D:126-194
1d
GHMP_kinases_N-1wuuD04
D:126-194
Clan
:
no clan defined [family: GHMP_kinases_C]
(13)
Family
:
GHMP_kinases_C
(13)
Homo sapiens (Human)
(2)
2a
GHMP_kinases_C-1wuuD05
D:291-374
2b
GHMP_kinases_C-1wuuD06
D:291-374
2c
GHMP_kinases_C-1wuuD07
D:291-374
2d
GHMP_kinases_C-1wuuD08
D:291-374
Clan
:
no clan defined [family: GalKase_gal_bdg]
(3)
Family
:
GalKase_gal_bdg
(3)
Homo sapiens (Human)
(1)
3a
GalKase_gal_bdg-1wuuD09
D:17-68
3b
GalKase_gal_bdg-1wuuD10
D:17-68
3c
GalKase_gal_bdg-1wuuD11
D:17-68
3d
GalKase_gal_bdg-1wuuD12
D:17-68
[
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Asym.Unit (263 KB)
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