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1WUU
Asym. Unit
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
(4, 44)
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
4
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
GLA
4
Ligand/Ion
ALPHA D-GALACTOSE
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
AC3
SOFTWARE
ARG C:37 , GLU C:43 , HIS C:44 , ASP C:46 , TYR C:47 , CYS C:182 , GLY C:183 , MSE C:185 , ASP C:186 , TYR C:236 , GLY C:346 , ANP C:395 , HOH C:446
BINDING SITE FOR RESIDUE GLA C 393
04
AC4
SOFTWARE
ARG D:37 , GLU D:43 , HIS D:44 , ASP D:46 , TYR D:47 , CYS D:182 , GLY D:183 , MSE D:185 , ASP D:186 , TYR D:236 , GLY D:346 , ANP D:395 , HOH D:439
BINDING SITE FOR RESIDUE GLA D 393
05
AC5
SOFTWARE
SER A:140 , SER A:142 , GLA A:393 , ANP A:395
BINDING SITE FOR RESIDUE MG A 394
06
AC6
SOFTWARE
SER B:142 , ASP B:186 , ANP B:395
BINDING SITE FOR RESIDUE MG B 394
07
AC7
SOFTWARE
SER C:142 , GLU C:174 , ANP C:395
BINDING SITE FOR RESIDUE MG C 394
08
AC8
SOFTWARE
SER D:142 , GLU D:174 , ASP D:186 , ANP D:395
BINDING SITE FOR RESIDUE MG D 394
09
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
10
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
11
BC2
SOFTWARE
ARG C:37 , THR C:77 , ALA C:82 , TRP C:106 , TYR C:109 , VAL C:129 , SER C:131 , LEU C:135 , GLY C:136 , GLY C:138 , LEU C:139 , SER C:140 , SER C:141 , SER C:142 , LEU C:145 , ARG C:228 , GLY C:346 , GLA C:393 , MG C:394 , HOH C:406 , HOH C:438 , HOH C:439 , HOH C:443 , HOH C:463
BINDING SITE FOR RESIDUE ANP C 395
12
BC3
SOFTWARE
ARG D:37 , THR D:77 , TRP D:106 , TYR D:109 , VAL D:129 , LEU D:135 , GLY D:136 , GLY D:137 , GLY D:138 , LEU D:139 , SER D:140 , SER D:141 , SER D:142 , LEU D:145 , GLY D:346 , GLA D:393 , MG D:394 , HOH D:434 , HOH D:436
BINDING SITE FOR RESIDUE ANP D 395
[
close Site info
]
SAPs(SNPs)/Variants
(14, 56)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_008514 (P28T, chain A/B/C/D, )
02: VAR_002547 (V32M, chain A/B/C/D, )
03: VAR_023486 (G36R, chain A/B/C/D, )
04: VAR_023487 (H44Y, chain A/B/C/D, )
05: VAR_023488 (R68C, chain A/B/C/D, )
06: VAR_023489 (I184M, chain A/B/C/D, )
07: VAR_015746 (A198V, chain A/B/C/D, )
08: VAR_023490 (R239Q, chain A/B/C/D, )
09: VAR_023491 (G274D, chain A/B/C/D, )
10: VAR_023492 (T288M, chain A/B/C/D, )
11: VAR_023493 (V338A, chain A/B/C/D, )
12: VAR_023494 (G346S, chain A/B/C/D, )
13: VAR_023495 (G349S, chain A/B/C/D, )
14: VAR_023496 (A384P, chain A/B/C/D, )
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/C/D
P
28
T
02
UniProt
VAR_002547
V
32
M
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
V
32
M
03
UniProt
VAR_023486
G
36
R
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
G
36
R
04
UniProt
VAR_023487
H
44
Y
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
H
44
Y
05
UniProt
VAR_023488
R
68
C
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
R
68
C
06
UniProt
VAR_023489
I
184
M
GALK1_HUMAN
Polymorphism
---
A/B/C/D
I
184
M
07
UniProt
VAR_015746
A
198
V
GALK1_HUMAN
Disease (GALCT2)
80084721
A/B/C/D
A
198
V
08
UniProt
VAR_023490
R
239
Q
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
R
239
Q
09
UniProt
VAR_023491
G
274
D
GALK1_HUMAN
Polymorphism
---
A/B/C/D
G
274
D
10
UniProt
VAR_023492
T
288
M
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
T
288
M
11
UniProt
VAR_023493
V
338
A
GALK1_HUMAN
Polymorphism
---
A/B/C/D
V
338
A
12
UniProt
VAR_023494
G
346
S
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
G
346
S
13
UniProt
VAR_023495
G
349
S
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
G
349
S
14
UniProt
VAR_023496
A
384
P
GALK1_HUMAN
Disease (GALCT2)
---
A/B/C/D
A
384
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: GALACTOKINASE (A:36-47,B:36-47,C:36-47,D:36-47)
2: GHMP_KINASES_ATP (A:133-144,B:133-144,C:133-144,D:13...)
;
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
4
A:36-47
B:36-47
C:36-47
D:36-47
2
GHMP_KINASES_ATP
PS00627
GHMP kinases putative ATP-binding domain.
GALK1_HUMAN
133-144
4
A:133-144
B:133-144
C:133-144
D:133-144
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.1b (A:1-55 | B:2-55 | C:1-55 | D:1-55)
Exon 1.5a (A:56-119 | B:56-119 | C:56-119 | D...)
Exon 1.6 (A:119-159 | B:119-159 | C:119-159 ...)
Exon 1.7 (A:159-204 | B:159-204 | C:159-204 ...)
Exon 1.8 (A:204-265 (gaps) | B:204-265 (gaps...)
Exon 1.9b (A:265-315 | B:265-315 | C:265-315 ...)
Exon 1.10 (A:315-369 | B:315-369 | C:315-369 ...)
Exon 1.11b (A:370-392 | B:370-392 | C:370-392 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.5a
3: Boundary 1.5a/1.6
4: Boundary 1.6/1.7
5: Boundary 1.7/1.8
6: Boundary 1.8/1.9b
7: Boundary 1.9b/1.10
8: Boundary 1.10/1.11b
9: Boundary 1.11b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000225614
1b
ENSE00001303886
chr17:
73761280-73761053
228
GALK1_HUMAN
1-55
55
4
A:1-55
B:2-55
C:1-55
D:1-55
55
54
55
55
1.5a
ENST00000225614
5a
ENSE00000744749
chr17:
73760167-73759978
190
GALK1_HUMAN
56-119
64
4
A:56-119
B:56-119
C:56-119
D:56-119
64
64
64
64
1.6
ENST00000225614
6
ENSE00000744747
chr17:
73759520-73759401
120
GALK1_HUMAN
119-159
41
4
A:119-159
B:119-159
C:119-159
D:119-159
41
41
41
41
1.7
ENST00000225614
7
ENSE00000744745
chr17:
73759230-73759095
136
GALK1_HUMAN
159-204
46
4
A:159-204
B:159-204
C:159-204
D:159-204
46
46
46
46
1.8
ENST00000225614
8
ENSE00000744743
chr17:
73758966-73758785
182
GALK1_HUMAN
204-265
62
4
A:204-265 (gaps)
B:204-265 (gaps)
C:204-265 (gaps)
D:204-265 (gaps)
62
62
62
62
1.9b
ENST00000225614
9b
ENSE00000744742
chr17:
73754680-73754530
151
GALK1_HUMAN
265-315
51
4
A:265-315
B:265-315
C:265-315
D:265-315
51
51
51
51
1.10
ENST00000225614
10
ENSE00000744741
chr17:
73754453-73754291
163
GALK1_HUMAN
315-369
55
4
A:315-369
B:315-369
C:315-369
D:315-369
55
55
55
55
1.11b
ENST00000225614
11b
ENSE00001320710
chr17:
73754208-73754018
191
GALK1_HUMAN
370-392
23
4
A:370-392
B:370-392
C:370-392
D:370-392
23
23
23
23
[
close EXON info
]
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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Families
(
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(
)
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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Architectures
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(
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Topologies
(
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(
)
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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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
[
close Pfam info
]
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select chains 'A' and 'C'
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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).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (263 KB)
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