PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3FHY
Asym. Unit
Info
Asym.Unit (115 KB)
Biol.Unit 1 (108 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF D235N MUTANT OF HUMAN PYRIDOXAL KINASE
Authors
:
M. K. Safo, A. K. Gandhi, F. N. Musayev, M. Ghatge, M. L. Di Salvo, V. Schirch
Date
:
10 Dec 08 (Deposition) - 23 Dec 08 (Release) - 21 Apr 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Beta Sheet With Alpha Helix, Atp Complex, Metal Ion, Transferase, Acetylation, Alternative Splicing, Atp-Binding, Cytoplasm, Kinase, Metal-Binding, Nucleotide-Binding, Zinc
(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
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 26)
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)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
5l: SULFATE ION (SO4l)
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
8
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
NA
2
Ligand/Ion
SODIUM ION
5
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(26, 26)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:118 , SO4 A:316 , HOH A:320 , ATP A:409 , HOH A:418
BINDING SITE FOR RESIDUE MG A 400
02
AC2
SOFTWARE
ASP A:113 , THR A:148 , PRO A:149 , ASN A:150 , GLU A:153 , THR A:186 , ATP A:409 , HOH A:419
BINDING SITE FOR RESIDUE NA A 402
03
AC3
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 , VAL A:226 , ALA A:228 , THR A:233 , GLY A:234 , LEU A:263 , LEU A:267 , SO4 A:316 , SO4 A:317 , HOH A:325 , MG A:400 , NA A:402 , HOH A:417 , HOH A:418
BINDING SITE FOR RESIDUE ATP A 409
04
AC4
SOFTWARE
CYS A:5 , LEU A:31 , PHE A:33 , LYS A:247
BINDING SITE FOR RESIDUE SO4 A 313
05
AC5
SOFTWARE
GLU A:155 , LYS A:161
BINDING SITE FOR RESIDUE SO4 A 314
06
AC6
SOFTWARE
GLY A:179 , ASP A:181 , MPD A:318 , HOH A:345 , HOH A:369
BINDING SITE FOR RESIDUE SO4 A 315
07
AC7
SOFTWARE
MG A:400 , ATP A:409
BINDING SITE FOR RESIDUE SO4 A 316
08
AC8
SOFTWARE
GLY A:232 , THR A:233 , GLY A:234 , ASN A:235 , ATP A:409
BINDING SITE FOR RESIDUE SO4 A 317
09
AC9
SOFTWARE
ASP A:181 , ARG A:206 , ARG A:208 , SO4 A:315
BINDING SITE FOR RESIDUE MPD A 318
10
BC1
SOFTWARE
GLN A:63 , TYR A:66 , ARG A:70 , MET A:93 , ASP A:96 , GLU A:100
BINDING SITE FOR RESIDUE MPD A 319
11
BC2
SOFTWARE
ASP B:118 , SO4 B:318 , ATP B:407 , HOH B:419 , HOH B:422
BINDING SITE FOR RESIDUE MG B 404
12
BC3
SOFTWARE
ASP B:113 , THR B:148 , ASN B:150 , THR B:186 , ATP B:407 , HOH B:418
BINDING SITE FOR RESIDUE NA B 406
13
BC4
SOFTWARE
ASP B:113 , ASP B:118 , ASN B:150 , GLU B:153 , THR B:186 , SER B:187 , VAL B:201 , ARG B:224 , VAL B:226 , ALA B:228 , THR B:233 , GLY B:234 , LEU B:267 , SO4 B:318 , SO4 B:319 , HOH B:383 , MG B:404 , NA B:406 , HOH B:419
BINDING SITE FOR RESIDUE ATP B 407
14
BC5
SOFTWARE
ARG B:160
BINDING SITE FOR RESIDUE SO4 B 313
15
BC6
SOFTWARE
CYS B:5 , LEU B:31 , GLY B:32 , HIS B:246
BINDING SITE FOR RESIDUE SO4 B 314
16
BC7
SOFTWARE
VAL A:56 , GLU A:61 , VAL B:56 , GLU B:61 , HOH B:357 , HOH B:392
BINDING SITE FOR RESIDUE SO4 B 315
17
BC8
SOFTWARE
ARG B:70 , GLU B:100
BINDING SITE FOR RESIDUE SO4 B 316
18
BC9
SOFTWARE
ASP B:145 , GLY B:179 , ASP B:181 , HOH B:342 , HOH B:360
BINDING SITE FOR RESIDUE SO4 B 317
19
CC1
SOFTWARE
LEU B:199 , MG B:404 , ATP B:407
BINDING SITE FOR RESIDUE SO4 B 318
20
CC2
SOFTWARE
VAL B:231 , GLY B:232 , THR B:233 , GLY B:234 , ASN B:235 , ATP B:407
BINDING SITE FOR RESIDUE SO4 B 319
21
CC3
SOFTWARE
ASP B:181 , ARG B:207 , ARG B:208 , HOH B:326
BINDING SITE FOR RESIDUE MPD B 320
22
CC4
SOFTWARE
ASP B:173 , LEU B:312
BINDING SITE FOR RESIDUE MPD B 321
23
CC5
SOFTWARE
HIS B:248 , PRO B:249 , ASN B:250 , ASN B:251
BINDING SITE FOR RESIDUE MPD B 322
24
CC6
SOFTWARE
GLY B:124 , GLU B:130
BINDING SITE FOR RESIDUE MPD B 323
25
CC7
SOFTWARE
VAL B:19 , HIS B:46 , THR B:47 , VAL B:231 , HOH B:403
BINDING SITE FOR RESIDUE MPD B 324
26
CC8
SOFTWARE
PRO B:191 , PRO B:193 , ARG B:220
BINDING SITE FOR RESIDUE MPD B 325
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(11, 22)
Info
All Exons
Exon 1.1c (A:4-29 | 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:171-208 | 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 (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:4-29
B:4-29
26
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:171-208
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 (gaps)
37
37
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3fhya_ (A:)
1b: SCOP_d3fhyb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
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
d3fhya_
A:
1b
d3fhyb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3fhyA00 (A:4-312)
1b: CATH_3fhyB00 (B:4-312)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
3fhyA00
A:4-312
1b
3fhyB00
B:4-312
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
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)
[
close Script example commands
]
Log
Note:
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (115 KB)
Header - Asym.Unit
Biol.Unit 1 (108 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3FHY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help