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2YXU
Asym. Unit
Info
Asym.Unit (120 KB)
Biol.Unit 1 (113 KB)
Biol.Unit 2 (223 KB)
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(1)
Title
:
HUMAN PYRIDOXAL KINASE
Authors
:
M. K. Safo, F. N. Musayev, T. P. Ko, V. Schirch
Date
:
27 Apr 07 (Deposition) - 11 Mar 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Beta Sheet With Alpha Helix, Atp Complex, Metal Ion, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. N. Musayev, M. L. Di Salvo, T. P. Ko, A. K. Gandhi, A. Goswami, V. Schirch, M. K. Safo
Crystal Structure Of Human Pyridoxal Kinase: Structural Basis Of M(+) And M(2+) Activation.
Protein Sci. V. 16 2184 2007
[
close entry info
]
Hetero Components
(5, 23)
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)
3e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
3f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
3g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
3h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
3i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
3j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
3k: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDk)
3l: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDl)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
5d: PHOSPHATE ION (PO4d)
5e: PHOSPHATE ION (PO4e)
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
12
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
NA
2
Ligand/Ion
SODIUM ION
5
PO4
5
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:118 , HOH A:1506 , HOH A:1507
BINDING SITE FOR RESIDUE MG A 1404
02
AC2
SOFTWARE
ASP A:113 , THR A:148 , THR A:186 , HOH A:1508
BINDING SITE FOR RESIDUE NA A 1406
03
AC3
SOFTWARE
ASP B:118 , HOH B:2411 , HOH B:2412
BINDING SITE FOR RESIDUE MG B 2404
04
AC4
SOFTWARE
THR B:148 , THR B:186 , HOH B:2413
BINDING SITE FOR RESIDUE NA B 2406
05
AC5
SOFTWARE
CYS A:5 , LEU A:31 , GLY A:32
BINDING SITE FOR RESIDUE PO4 A 1501
06
AC6
SOFTWARE
LEU B:31 , GLY B:32 , HIS B:246
BINDING SITE FOR RESIDUE PO4 B 1517
07
AC7
SOFTWARE
GLN B:63 , GLU B:100
BINDING SITE FOR RESIDUE PO4 B 1527
08
AC8
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 , ALA A:228 , THR A:233 , GLY A:234 , LEU A:267 , HOH A:1506 , HOH A:1507 , HOH A:1510
BINDING SITE FOR RESIDUE ATP A 1410
09
AC9
SOFTWARE
ASP B:113 , ASP B:118 , TYR B:127 , THR B:148 , ASN B:150 , GLU B:153 , THR B:186 , SER B:187 , LEU B:199 , ARG B:224 , LYS B:225 , ALA B:228 , THR B:233 , GLY B:234 , LEU B:263 , LEU B:267 , HOH B:2411 , HOH B:2412 , HOH B:2419 , HOH B:2500 , HOH B:2540
BINDING SITE FOR RESIDUE ATP B 2410
10
BC1
SOFTWARE
TYR A:66 , ARG A:70 , MET A:93 , GLU A:100
BINDING SITE FOR RESIDUE MPD A 1011
11
BC2
SOFTWARE
SER A:12 , HIS A:46 , THR A:47 , TYR A:84 , HOH A:1602
BINDING SITE FOR RESIDUE MPD A 1013
12
BC3
SOFTWARE
PRO B:142 , ALA B:144 , ASP B:145 , GLY B:179 , PRO B:180 , ASP B:181 , HOH B:2438 , HOH B:2466
BINDING SITE FOR RESIDUE MPD B 1015
13
BC4
SOFTWARE
SER B:12 , HIS B:46 , THR B:47 , ASP B:235 , HOH B:2600
BINDING SITE FOR RESIDUE MPD B 1019
14
BC5
SOFTWARE
ASP B:181 , ARG B:208
BINDING SITE FOR RESIDUE MPD B 1021
15
BC6
SOFTWARE
SER B:177 , ARG B:206 , LEU B:312
BINDING SITE FOR RESIDUE MPD B 1023
16
BC7
SOFTWARE
HIS B:248 , PRO B:249 , ASN B:250 , ASN B:251 , HOH B:2546
BINDING SITE FOR RESIDUE MPD B 1025
17
BC8
SOFTWARE
GLU B:123 , GLY B:124
BINDING SITE FOR RESIDUE MPD B 1029
18
BC9
SOFTWARE
PRO A:191 , PHE B:43 , TYR B:84 , ARG B:86
BINDING SITE FOR RESIDUE MPD B 1031
19
CC1
SOFTWARE
ASP A:118 , HOH A:1507
BINDING SITE FOR RESIDUE MPD A 1037
20
CC2
SOFTWARE
ASP B:118 , HOH B:2412 , HOH B:2485 , HOH B:2500
BINDING SITE FOR RESIDUE MPD B 1039
21
CC3
SOFTWARE
PRO B:191 , HOH B:2441 , HOH B:2443
BINDING SITE FOR RESIDUE MPD B 1041
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
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:171-207 | B:171-208)
Exon 1.17c (A:212-253 | B:208-253)
Exon 1.18b (A:254-276 | B:254-276)
Exon 1.19e (A:276-312 | B:276-312 (gaps))
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:171-207
B:171-208
37
38
1.17c
ENST00000291565
17c
ENSE00001050587
chr21:
45173464-45173600
137
PDXK_HUMAN
208-253
46
2
A:212-253
B:208-253
42
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 (gaps)
37
37
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2yxua_ (A:)
1b: SCOP_d2yxub_ (B:)
View:
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d2yxua_
A:
1b
d2yxub_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2yxuA00 (A:3-312)
1b: CATH_2yxuB00 (B:3-312)
View:
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Classes
(
)
(
)
Architectures
(
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
2yxuA00
A:3-312
1b
2yxuB00
B:3-312
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PfkB_2yxuB01 (B:3-283)
1b: PFAM_PfkB_2yxuB02 (B:3-283)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ribokinase
(55)
Family
:
PfkB
(39)
Homo sapiens (Human)
(3)
1a
PfkB-2yxuB01
B:3-283
1b
PfkB-2yxuB02
B:3-283
[
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]
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