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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4CBR
Asym. Unit
Info
Asym.Unit (133 KB)
Biol.Unit 1 (255 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF THE MORE STABLE HUMAN AGXT TRIPLE MUTANT (AGXT_HEM)
Authors
:
C. Yunta, A. Albert
Date
:
16 Oct 13 (Deposition) - 09 Jul 14 (Release) - 03 Sep 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Transferase, Primary Hiperoxaluria Type I
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Mesa-Torres, C. Yunta, I. Fabelo-Rosa, J. M. Gonzalez-Rubio, J. M. Sanchez-Ruiz, E. Salido, A. Albert, A. L. Pey
The Consensus-Based Approach For Gene/Enzyme Replacement Therapies And Crystallization Strategies: The Case Of Human Alanine:Glyoxylate Aminotransferase.
Biochem. J. V. 462 453 2014
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
PLP
1
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:81 , GLY A:82 , HIS A:83 , TRP A:108 , GLY A:156 , SER A:158 , ASP A:183 , VAL A:185 , ALA A:186 , GLN A:208 , LYS A:209 , TYR A:260 , THR A:263 , GOL A:1390
BINDING SITE FOR RESIDUE PLP A1389
2
AC2
SOFTWARE
PRO A:28 , HIS A:48 , LYS A:209 , TYR A:260 , LEU A:351 , ARG A:360 , PLP A:1389 , HOH A:2088
BINDING SITE FOR RESIDUE GOL A1390
[
close Site info
]
SAPs(SNPs)/Variants
(41, 41)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_060547 (T9N, chain A, )
02: VAR_000587 (P11L, chain A, )
03: VAR_048236 (N22S, chain A, )
04: VAR_000588 (G41R, chain A, )
05: VAR_010969 (G41V, chain A, )
06: VAR_008878 (G82E, chain A, )
07: VAR_060548 (G82R, chain A, )
08: VAR_060549 (W108R, chain A, )
09: VAR_060550 (A112D, chain A, )
10: VAR_010971 (G116R, chain A, )
11: VAR_000589 (F152I, chain A, )
12: VAR_060552 (L153V, chain A, )
13: VAR_010972 (G156R, chain A, )
14: VAR_060553 (S158L, chain A, )
15: VAR_060554 (G161R, chain A, )
16: VAR_000590 (G170R, chain A, )
17: VAR_060555 (C173Y, chain A, )
18: VAR_010973 (D183N, chain A, )
19: VAR_000591 (S187F, chain A, )
20: VAR_060556 (G190R, chain A, )
21: VAR_060557 (M195R, chain A, )
22: VAR_060558 (D201E, chain A, )
23: VAR_000592 (S205P, chain A, )
24: VAR_060559 (S218L, chain A, )
25: VAR_008879 (R233C, chain A, )
26: VAR_008880 (R233H, chain A, )
27: VAR_060560 (R233L, chain A, )
28: VAR_060561 (D243H, chain A, )
29: VAR_008881 (I244T, chain A, )
30: VAR_060562 (C253R, chain A, )
31: VAR_060563 (I279M, chain A, )
32: VAR_060564 (I279T, chain A, )
33: VAR_060565 (A280V, chain A, )
34: VAR_060566 (S287T, chain A, )
35: VAR_060567 (R289C, chain A, )
36: VAR_048237 (A295T, chain A, )
37: VAR_060569 (L298P, chain A, )
38: VAR_060570 (V326I, chain A, )
39: VAR_060571 (V336D, chain A, )
40: VAR_000593 (M340M, chain A, )
41: VAR_060572 (G350D, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_060547
T
9
N
SPYA_HUMAN
Disease (HP1)
---
A
T
9
N
02
UniProt
VAR_000587
P
11
L
SPYA_HUMAN
Polymorphism
34116584
A
P
11
L
03
UniProt
VAR_048236
N
22
S
SPYA_HUMAN
Polymorphism
34885252
A
N
22
S
04
UniProt
VAR_000588
G
41
R
SPYA_HUMAN
Disease (HP1)
---
A
G
41
R
05
UniProt
VAR_010969
G
41
V
SPYA_HUMAN
Disease (HP1)
---
A
G
41
V
06
UniProt
VAR_008878
G
82
E
SPYA_HUMAN
Disease (HP1)
---
A
G
82
E
07
UniProt
VAR_060548
G
82
R
SPYA_HUMAN
Disease (HP1)
---
A
G
82
R
08
UniProt
VAR_060549
W
108
R
SPYA_HUMAN
Disease (HP1)
---
A
W
108
R
09
UniProt
VAR_060550
A
112
D
SPYA_HUMAN
Disease (HP1)
---
A
A
112
D
10
UniProt
VAR_010971
G
116
R
SPYA_HUMAN
Disease (HP1)
---
A
G
116
R
11
UniProt
VAR_000589
F
152
I
SPYA_HUMAN
Disease (HP1)
---
A
F
152
I
12
UniProt
VAR_060552
L
153
V
SPYA_HUMAN
Disease (HP1)
---
A
L
153
V
13
UniProt
VAR_010972
G
156
R
SPYA_HUMAN
Disease (HP1)
---
A
G
156
R
14
UniProt
VAR_060553
S
158
L
SPYA_HUMAN
Disease (HP1)
---
A
S
158
L
15
UniProt
VAR_060554
G
161
R
SPYA_HUMAN
Disease (HP1)
---
A
G
161
R
16
UniProt
VAR_000590
G
170
R
SPYA_HUMAN
Disease (HP1)
---
A
G
170
R
17
UniProt
VAR_060555
C
173
Y
SPYA_HUMAN
Disease (HP1)
---
A
C
173
Y
18
UniProt
VAR_010973
D
183
N
SPYA_HUMAN
Disease (HP1)
---
A
D
183
N
19
UniProt
VAR_000591
S
187
F
SPYA_HUMAN
Disease (HP1)
---
A
S
187
F
20
UniProt
VAR_060556
G
190
R
SPYA_HUMAN
Disease (HP1)
---
A
G
190
R
21
UniProt
VAR_060557
M
195
R
SPYA_HUMAN
Disease (HP1)
---
A
M
195
R
22
UniProt
VAR_060558
D
201
E
SPYA_HUMAN
Disease (HP1)
---
A
D
201
E
23
UniProt
VAR_000592
S
205
P
SPYA_HUMAN
Disease (HP1)
---
A
S
205
P
24
UniProt
VAR_060559
S
218
L
SPYA_HUMAN
Disease (HP1)
---
A
S
218
L
25
UniProt
VAR_008879
R
233
C
SPYA_HUMAN
Disease (HP1)
---
A
R
233
C
26
UniProt
VAR_008880
R
233
H
SPYA_HUMAN
Disease (HP1)
---
A
R
233
H
27
UniProt
VAR_060560
R
233
L
SPYA_HUMAN
Disease (HP1)
---
A
R
233
L
28
UniProt
VAR_060561
D
243
H
SPYA_HUMAN
Disease (HP1)
---
A
D
243
H
29
UniProt
VAR_008881
I
244
T
SPYA_HUMAN
Disease (HP1)
---
A
I
244
T
30
UniProt
VAR_060562
C
253
R
SPYA_HUMAN
Disease (HP1)
---
A
C
253
R
31
UniProt
VAR_060563
I
279
M
SPYA_HUMAN
Disease (HP1)
---
A
I
279
M
32
UniProt
VAR_060564
I
279
T
SPYA_HUMAN
Polymorphism
140992177
A
I
279
T
33
UniProt
VAR_060565
A
280
V
SPYA_HUMAN
Polymorphism
73106685
A
A
280
V
34
UniProt
VAR_060566
S
287
T
SPYA_HUMAN
Disease (HP1)
---
A
S
287
T
35
UniProt
VAR_060567
R
289
C
SPYA_HUMAN
Disease (HP1)
---
A
R
289
C
36
UniProt
VAR_048237
A
295
T
SPYA_HUMAN
Polymorphism
13408961
A
A
295
T
37
UniProt
VAR_060569
L
298
P
SPYA_HUMAN
Disease (HP1)
---
A
L
298
P
38
UniProt
VAR_060570
V
326
I
SPYA_HUMAN
Polymorphism
115057148
A
V
326
I
39
UniProt
VAR_060571
V
336
D
SPYA_HUMAN
Disease (HP1)
---
A
V
336
D
40
UniProt
VAR_000593
I
340
M
SPYA_HUMAN
Polymorphism
4426527
A
M
340
M
41
UniProt
VAR_060572
G
350
D
SPYA_HUMAN
Disease (HP1)
---
A
G
350
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: AA_TRANSFER_CLASS_5 (A:200-220)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRANSFER_CLASS_5
PS00595
Aminotransferases class-V pyridoxal-phosphate attachment site.
SPYA_HUMAN
200-220
1
A:200-220
[
close PROSITE info
]
Exons
(11, 11)
Info
All Exons
Exon 1.1a (A:4-55)
Exon 1.2 (A:56-120)
Exon 1.3 (A:120-141)
Exon 1.4b (A:142-175)
Exon 1.5a (A:175-199)
Exon 1.6 (A:199-227)
Exon 1.7 (A:227-259)
Exon 1.8a (A:259-282)
Exon 1.9b (A:283-314)
Exon 1.10 (A:315-357)
Exon 1.11a (A:358-388)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4b
05: Boundary 1.4b/1.5a
06: Boundary 1.5a/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8a
09: Boundary 1.8a/1.9b
10: Boundary 1.9b/1.10
11: Boundary 1.10/1.11a
12: Boundary 1.11a/-
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
1.1a
ENST00000307503
1a
ENSE00001843474
chr2:
241807896-241808447
552
SPYA_HUMAN
1-55
55
1
A:4-55
52
1.2
ENST00000307503
2
ENSE00001162366
chr2:
241808587-241808779
193
SPYA_HUMAN
56-120
65
1
A:56-120
65
1.3
ENST00000307503
3
ENSE00001162358
chr2:
241810061-241810125
65
SPYA_HUMAN
120-141
22
1
A:120-141
22
1.4b
ENST00000307503
4b
ENSE00001162348
chr2:
241810766-241810866
101
SPYA_HUMAN
142-175
34
1
A:142-175
34
1.5a
ENST00000307503
5a
ENSE00001162341
chr2:
241812396-241812466
71
SPYA_HUMAN
175-199
25
1
A:175-199
25
1.6
ENST00000307503
6
ENSE00001162333
chr2:
241813395-241813479
85
SPYA_HUMAN
199-227
29
1
A:199-227
29
1.7
ENST00000307503
7
ENSE00001162328
chr2:
241814526-241814621
96
SPYA_HUMAN
227-259
33
1
A:227-259
33
1.8a
ENST00000307503
8a
ENSE00001162322
chr2:
241815352-241815421
70
SPYA_HUMAN
259-282
24
1
A:259-282
24
1.9b
ENST00000307503
9b
ENSE00001162318
chr2:
241816954-241817049
96
SPYA_HUMAN
283-314
32
1
A:283-314
32
1.10
ENST00000307503
10
ENSE00001162312
chr2:
241817439-241817567
129
SPYA_HUMAN
315-357
43
1
A:315-357
43
1.11a
ENST00000307503
11a
ENSE00001895938
chr2:
241818131-241818537
407
SPYA_HUMAN
358-392
35
1
A:358-388
31
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (133 KB)
Header - Asym.Unit
Biol.Unit 1 (255 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
4CBR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help