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3KEU
Asym. Unit
Info
Asym.Unit (117 KB)
Biol.Unit 1 (111 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PL KINASE WITH BOUND PLP AND ATP
Authors
:
M. K. Safo, A. K. Gandhi, F. N. Musayev
Date
:
26 Oct 09 (Deposition) - 03 Nov 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Pyridoxal 5'-Phosphate, Pyridoxal Kinase, Vitamin B6, Plp, Atp- Binding, Kinase, Metal-Binding, Nucleotide-Binding, Phosphoprotein, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. K. Gandhi, F. N. Musayev, M. K. Safo
Crystal Structure Of Pl Kinase In Complex With Mgatp And Plp: Structural Basis Of Severe Induced Mgatp Substrate Inhibition Of The Enzyme
To Be Published
[
close entry info
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Hetero Components
(6, 27)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
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)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
5b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
MPD
9
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
NA
2
Ligand/Ion
SODIUM ION
5
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
6
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(27, 27)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:118 , ATP A:407 , MPD A:512 , HOH A:792 , HOH A:806
BINDING SITE FOR RESIDUE MG A 400
02
AC2
SOFTWARE
ASP A:235 , ATP A:407 , PLP A:500
BINDING SITE FOR RESIDUE MG A 401
03
AC3
SOFTWARE
ASP A:113 , THR A:148 , THR A:186 , ATP A:407 , HOH A:656
BINDING SITE FOR RESIDUE NA A 402
04
AC4
SOFTWARE
ASP A:113 , ASP A:118 , ASN A:150 , GLU A:153 , THR A:186 , SER A:187 , VAL A:201 , ARG A:224 , LYS A:225 , VAL A:226 , ALA A:228 , THR A:233 , GLY A:234 , LEU A:267 , MG A:400 , MG A:401 , NA A:402 , PLP A:500 , MPD A:512 , HOH A:792 , HOH A:805 , HOH A:806 , HOH A:824 , HOH A:849
BINDING SITE FOR RESIDUE ATP A 407
05
AC5
SOFTWARE
SER A:12 , VAL A:19 , GLY A:20 , THR A:47 , VAL A:231 , GLY A:232 , THR A:233 , GLY A:234 , ASP A:235 , MG A:401 , ATP A:407
BINDING SITE FOR RESIDUE PLP A 500
06
AC6
SOFTWARE
SER A:12 , THR A:47 , TYR A:84
BINDING SITE FOR RESIDUE MPD A 508
07
AC7
SOFTWARE
ASP A:118 , LEU A:199 , MG A:400 , ATP A:407 , HOH A:822
BINDING SITE FOR RESIDUE MPD A 512
08
AC8
SOFTWARE
LYS A:76 , ASP A:78 , ASN A:105 , HOH A:907
BINDING SITE FOR RESIDUE MPD A 516
09
AC9
SOFTWARE
GLU A:155
BINDING SITE FOR RESIDUE SO4 A 524
10
BC1
SOFTWARE
GLN A:63 , ARG A:70 , MET A:93 , GLU A:100
BINDING SITE FOR RESIDUE SO4 A 528
11
BC2
SOFTWARE
CYS A:5 , LEU A:31 , GLY A:32 , LYS A:247
BINDING SITE FOR RESIDUE SO4 A 538
12
BC3
SOFTWARE
ASP B:118 , ATP B:409 , MPD B:514 , HOH B:797 , HOH B:798
BINDING SITE FOR RESIDUE MG B 404
13
BC4
SOFTWARE
VAL B:115 , ASP B:235 , ATP B:409 , PLP B:500
BINDING SITE FOR RESIDUE MG B 405
14
BC5
SOFTWARE
ASP B:113 , THR B:148 , PRO B:149 , ASN B:150 , THR B:186 , ATP B:409 , HOH B:796
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 , VAL B:201 , ARG B:224 , LYS B:225 , VAL B:226 , ALA B:228 , THR B:233 , GLY B:234 , LEU B:263 , LEU B:267 , MG B:404 , MG B:405 , NA B:406 , PLP B:500 , MPD B:514 , HOH B:766 , HOH B:797 , HOH B:846
BINDING SITE FOR RESIDUE ATP B 409
16
BC7
SOFTWARE
SER B:12 , VAL B:19 , HIS B:46 , THR B:47 , VAL B:231
BINDING SITE FOR RESIDUE MPD B 508
17
BC8
SOFTWARE
SER B:12 , VAL B:19 , GLY B:20 , THR B:47 , PHE B:230 , VAL B:231 , GLY B:232 , THR B:233 , GLY B:234 , ASP B:235 , MG B:405 , ATP B:409
BINDING SITE FOR RESIDUE PLP B 500
18
BC9
SOFTWARE
ASP B:181 , ARG B:206 , ARG B:207 , ARG B:208 , HOH B:842
BINDING SITE FOR RESIDUE MPD B 510
19
CC1
SOFTWARE
ASP B:118 , LYS B:225 , MG B:404 , ATP B:409 , HOH B:798 , HOH B:884
BINDING SITE FOR RESIDUE MPD B 514
20
CC2
SOFTWARE
SER B:177 , LEU B:312 , MPD B:520 , HOH B:785
BINDING SITE FOR RESIDUE MPD B 518
21
CC3
SOFTWARE
ASP B:173 , SER B:177 , ARG B:206 , LEU B:312 , MPD B:518 , HOH B:785
BINDING SITE FOR RESIDUE MPD B 520
22
CC4
SOFTWARE
GLN B:165
BINDING SITE FOR RESIDUE MPD B 522
23
CC5
SOFTWARE
GLN B:63 , GLU B:100
BINDING SITE FOR RESIDUE SO4 B 526
24
CC6
SOFTWARE
GLU B:4 , CYS B:5 , ASP B:78 , HIS B:246 , HOH B:869
BINDING SITE FOR RESIDUE SO4 B 530
25
CC7
SOFTWARE
GLU B:155 , ARG B:160
BINDING SITE FOR RESIDUE SO4 B 532
26
CC8
SOFTWARE
LEU B:31 , GLY B:32 , HIS B:246
BINDING SITE FOR RESIDUE SO4 B 534
27
CC9
SOFTWARE
TYR B:84 , HOH B:896
BINDING SITE FOR RESIDUE SO4 B 536
[
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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:4-29)
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:213-253 | 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:4-29
27
26
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:213-253
B:208-253
41
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
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3keua_ (A:)
1b: SCOP_d3keub_ (B:)
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Protein Domains
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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
d3keua_
A:
1b
d3keub_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3keuA00 (A:3-312)
1b: CATH_3keuB00 (B:4-312)
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Organisms
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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
3keuA00
A:3-312
1b
3keuB00
B:4-312
[
close CATH info
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PfkB_3keuB01 (B:4-283)
1b: PFAM_PfkB_3keuB02 (B:4-283)
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)
Clan
:
Ribokinase
(55)
Family
:
PfkB
(39)
Homo sapiens (Human)
(3)
1a
PfkB-3keuB01
B:4-283
1b
PfkB-3keuB02
B:4-283
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Asym.Unit (117 KB)
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