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3FHX
Asym. Unit
Info
Asym.Unit (114 KB)
Biol.Unit 1 (107 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D235A MUTANT OF HUMAN PYRIDOXAL KINASE
Authors
:
M. K. Safo, A. K. Gandhi, F. N. Musayev, M. Ghatge, M. L. Di Salvo, V. Schi
Date
:
10 Dec 08 (Deposition) - 23 Dec 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Beta Sheet With Alpha Helix, Atp Complex, Metal Ion, Transferase, Atp-Binding, Kinase, Metal-Binding, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. K. Gandhi, M. S. Ghatge, F. N. Musayev, A. Sease, S. O. Aboagye, M. L. Di Salvo, V. Schirch, M. K. Safo
Kinetic And Structural Studies Of The Role Of The Active Site Residue Asp235 Of Human Pyridoxal Kinase.
Biochem. Biophys. Res. Commun. V. 381 12 2009
[
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Hetero Components
(7, 24)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
6a: 3-HYDROXY-5-(HYDROXYMETHYL)-2-METH... (PXLa)
6b: 3-HYDROXY-5-(HYDROXYMETHYL)-2-METH... (PXLb)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
7e: SULFATE ION (SO4e)
7f: SULFATE ION (SO4f)
7g: SULFATE ION (SO4g)
7h: SULFATE ION (SO4h)
7i: SULFATE ION (SO4i)
7j: SULFATE ION (SO4j)
7k: SULFATE ION (SO4k)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
MPD
4
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
NA
2
Ligand/Ion
SODIUM ION
5
PLP
1
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
6
PXL
2
Ligand/Ion
3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
7
SO4
11
Ligand/Ion
SULFATE ION
[
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]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:118 , SO4 A:315 , HOH A:389 , HOH A:390 , ATP A:407
BINDING SITE FOR RESIDUE MG A 400
02
AC2
SOFTWARE
ASP A:113 , THR A:148 , PRO A:149 , ASN A:150 , THR A:186 , HOH A:392 , ATP A:407
BINDING SITE FOR RESIDUE NA A 402
03
AC3
SOFTWARE
ASP A:113 , ASP A:118 , TYR A:127 , ASN A:150 , GLU A:153 , THR A:186 , SER A:187 , ARG A:224 , LYS A:225 , VAL A:226 , ALA A:228 , THR A:233 , LEU A:267 , SO4 A:314 , SO4 A:315 , HOH A:349 , HOH A:389 , HOH A:390 , HOH A:392 , MG A:400 , NA A:402
BINDING SITE FOR RESIDUE ATP A 407
04
AC4
SOFTWARE
SER A:12 , HIS A:46 , THR A:47 , VAL A:231 , SO4 A:314 , HOH A:342 , HOH A:367
BINDING SITE FOR RESIDUE PXL A 313
05
AC5
SOFTWARE
VAL A:231 , GLY A:232 , GLY A:234 , ALA A:235 , PXL A:313 , HOH A:342 , ATP A:407
BINDING SITE FOR RESIDUE SO4 A 314
06
AC6
SOFTWARE
LEU A:199 , HOH A:390 , MG A:400 , ATP A:407
BINDING SITE FOR RESIDUE SO4 A 315
07
AC7
SOFTWARE
ARG A:70 , MET A:93 , GLU A:100
BINDING SITE FOR RESIDUE SO4 A 316
08
AC8
SOFTWARE
GLU A:3 , GLU A:4 , CYS A:5 , ASP A:78 , HIS A:246 , HOH A:383
BINDING SITE FOR RESIDUE SO4 A 317
09
AC9
SOFTWARE
GLY A:32 , LYS A:247
BINDING SITE FOR RESIDUE SO4 A 318
10
BC1
SOFTWARE
ASP A:145 , GLY A:179 , ASP A:181 , MPD A:321 , HOH A:334
BINDING SITE FOR RESIDUE SO4 A 319
11
BC2
SOFTWARE
VAL A:56 , GLU A:61 , HOH A:340 , GLU B:61 , GLU B:280
BINDING SITE FOR RESIDUE SO4 A 320
12
BC3
SOFTWARE
ASP A:181 , SO4 A:319
BINDING SITE FOR RESIDUE MPD A 321
13
BC4
SOFTWARE
ASP B:118 , SO4 B:315 , HOH B:344 , HOH B:383 , ATP B:409
BINDING SITE FOR RESIDUE MG B 404
14
BC5
SOFTWARE
ASP B:113 , THR B:148 , PRO B:149 , ASN B:150 , GLU B:153 , THR B:186 , HOH B:385 , ATP B:409
BINDING SITE FOR RESIDUE NA B 406
15
BC6
SOFTWARE
ASP B:113 , ASP B:118 , TYR B:127 , ASN B:150 , GLU B:153 , THR B:186 , SER B:187 , LEU B:199 , ARG B:224 , LYS B:225 , VAL B:226 , ALA B:228 , THR B:233 , LEU B:263 , LEU B:267 , PLP B:314 , SO4 B:315 , HOH B:344 , HOH B:353 , MG B:404 , NA B:406
BINDING SITE FOR RESIDUE ATP B 409
16
BC7
SOFTWARE
SER B:12 , VAL B:19 , PHE B:43 , ASN B:45 , HIS B:46 , THR B:47 , GLY B:48 , VAL B:231 , PLP B:314
BINDING SITE FOR RESIDUE PXL B 313
17
BC8
SOFTWARE
VAL B:231 , GLY B:232 , THR B:233 , GLY B:234 , PXL B:313 , HOH B:384 , ATP B:409
BINDING SITE FOR RESIDUE PLP B 314
18
BC9
SOFTWARE
HOH B:359 , MG B:404 , ATP B:409
BINDING SITE FOR RESIDUE SO4 B 315
19
CC1
SOFTWARE
GLN B:63 , ARG B:70 , GLU B:100
BINDING SITE FOR RESIDUE SO4 B 316
20
CC2
SOFTWARE
ALA B:144 , ASP B:145 , GLY B:179 , ASP B:181
BINDING SITE FOR RESIDUE SO4 B 317
21
CC3
SOFTWARE
GLN B:165 , HOH B:351
BINDING SITE FOR RESIDUE SO4 B 318
22
CC4
SOFTWARE
ARG A:170 , GLY B:124 , GLU B:130
BINDING SITE FOR RESIDUE MPD B 319
23
CC5
SOFTWARE
ASP B:173 , SER B:177 , LEU B:312
BINDING SITE FOR RESIDUE MPD B 320
24
CC6
SOFTWARE
ASP B:181 , ARG B:206 , ARG B:208
BINDING SITE FOR RESIDUE MPD B 321
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(11, 22)
Info
All Exons
Exon 1.1c (A:3-29 | B:3-29)
Exon 1.6 (A:30-48 | B:30-48)
Exon 1.9e (A:48-83 | B:48-83)
Exon 1.10b (A:83-111 | B:83-111)
Exon 1.12b (A:111-126 | B:111-126)
Exon 1.14 (A:127-155 | B:127-155)
Exon 1.15 (A:155-170 | B:155-170)
Exon 1.16 (A:171-208 | B:171-208)
Exon 1.17c (A:208-253 (gaps) | B:208-253)
Exon 1.18b (A:254-276 | B:254-276)
Exon 1.19e (A:276-312 | B:276-312)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1c
02: Boundary 1.1c/1.6
03: Boundary 1.6/1.9e
04: Boundary 1.9e/1.10b
05: Boundary 1.10b/1.12b
06: Boundary 1.12b/1.14
07: Boundary 1.14/1.15
08: Boundary 1.15/1.16
09: Boundary 1.16/1.17c
10: Boundary 1.17c/1.18b
11: Boundary 1.18b/1.19e
12: Boundary 1.19e/-
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
1.1c
ENST00000291565
1c
ENSE00001861574
chr21:
45138993-45139262
270
PDXK_HUMAN
1-29
29
2
A:3-29
B:3-29
27
27
1.6
ENST00000291565
6
ENSE00001050589
chr21:
45153950-45154004
55
PDXK_HUMAN
30-48
19
2
A:30-48
B:30-48
19
19
1.9e
ENST00000291565
9e
ENSE00001050594
chr21:
45161548-45161652
105
PDXK_HUMAN
48-83
36
2
A:48-83
B:48-83
36
36
1.10b
ENST00000291565
10b
ENSE00001050590
chr21:
45163605-45163688
84
PDXK_HUMAN
83-111
29
2
A:83-111
B:83-111
29
29
1.12b
ENST00000291565
12b
ENSE00001050584
chr21:
45165960-45166006
47
PDXK_HUMAN
111-126
16
2
A:111-126
B:111-126
16
16
1.14
ENST00000291565
14
ENSE00001050578
chr21:
45168876-45168961
86
PDXK_HUMAN
127-155
29
2
A:127-155
B:127-155
29
29
1.15
ENST00000291565
15
ENSE00001050582
chr21:
45170381-45170426
46
PDXK_HUMAN
155-170
16
2
A:155-170
B:155-170
16
16
1.16
ENST00000291565
16
ENSE00001050593
chr21:
45172399-45172510
112
PDXK_HUMAN
171-208
38
2
A:171-208
B:171-208
38
38
1.17c
ENST00000291565
17c
ENSE00001050587
chr21:
45173464-45173600
137
PDXK_HUMAN
208-253
46
2
A:208-253 (gaps)
B:208-253
46
46
1.18b
ENST00000291565
18b
ENSE00001050583
chr21:
45175579-45175645
67
PDXK_HUMAN
254-276
23
2
A:254-276
B:254-276
23
23
1.19e
ENST00000291565
19e
ENSE00001431057
chr21:
45175832-45182188
6357
PDXK_HUMAN
276-312
37
2
A:276-312
B:276-312
37
37
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3fhxa_ (A:)
1b: SCOP_d3fhxb_ (B:)
View:
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Classes
(
)
(
)
Folds
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(
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)
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribokinase-like
(226)
Superfamily
:
Ribokinase-like
(189)
Family
:
PfkB-like kinase
(20)
Protein domain
:
automated matches
(10)
Human (Homo sapiens) [TaxId: 9606]
(9)
1a
d3fhxa_
A:
1b
d3fhxb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3fhxA00 (A:3-312)
1b: CATH_3fhxB00 (B:3-312)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
(109)
Homologous Superfamily
:
[code=3.40.1190.20, no name defined]
(73)
Human (Homo sapiens)
(10)
1a
3fhxA00
A:3-312
1b
3fhxB00
B:3-312
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (114 KB)
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