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3R9A
Biol. Unit 1
Info
Asym.Unit (454 KB)
Biol.Unit 1 (447 KB)
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(1)
Title
:
HUMAN ALANINE-GLYOXYLATE AMINOTRANSFERASE IN COMPLEX WITH THE TPR DOMAIN OF HUMAN PEX5P
Authors
:
K. Fodor, M. Wilmanns
Date
:
25 Mar 11 (Deposition) - 11 May 11 (Release) - 02 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Tpr-Domain, Protein-Protein Complex, Peroxisome, Aminotransf Pyruvate, Transferase, Disease Mutation, Membrane, Peroxiso Biogenesis Disorder, Protein Transport, Tpr Repeat, Transpo Zellweger Syndrome, Transferase-Transport Protein Complex, Mitochondrion, Pyridoxal Phosphate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Fodor, J. Wolf, R. Erdmann, W. Schliebs, M. Wilmanns
Molecular Requirements For Peroxisomal Targeting Of Alanine-Glyoxylate Aminotransferase As An Essential Determinant In Primary Hyperoxaluria Type 1
Plos Biol. V. 10 01309 2012
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-... (BTBa)
2a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
2b: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BTB
1
Ligand/Ion
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2
LLP
2
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP C:246 , ASN C:249 , MET C:259
BINDING SITE FOR RESIDUE BTB C 393
[
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SAPs(SNPs)/Variants
(43, 86)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_060547 (T9N, chain A/C, )
02: VAR_000587 (P11L, chain A/C, )
03: VAR_048236 (N22S, chain A/C, )
04: VAR_000588 (G41R, chain A/C, )
05: VAR_010969 (G41V, chain A/C, )
06: VAR_008878 (G82E, chain A/C, )
07: VAR_060548 (G82R, chain A/C, )
08: VAR_060549 (W108R, chain A/C, )
09: VAR_060550 (A112D, chain A/C, )
10: VAR_010971 (G116R, chain A/C, )
11: VAR_000589 (F152I, chain A/C, )
12: VAR_060552 (L153V, chain A/C, )
13: VAR_010972 (G156R, chain A/C, )
14: VAR_060553 (S158L, chain A/C, )
15: VAR_060554 (G161R, chain A/C, )
16: VAR_000590 (G170R, chain A/C, )
17: VAR_060555 (C173Y, chain A/C, )
18: VAR_010973 (D183N, chain A/C, )
19: VAR_000591 (S187F, chain A/C, )
20: VAR_060556 (G190R, chain A/C, )
21: VAR_060557 (M195R, chain A/C, )
22: VAR_060558 (D201E, chain A/C, )
23: VAR_000592 (S205P, chain A/C, )
24: VAR_060559 (S218L, chain A/C, )
25: VAR_008879 (R233C, chain A/C, )
26: VAR_008880 (R233H, chain A/C, )
27: VAR_060560 (R233L, chain A/C, )
28: VAR_060561 (D243H, chain A/C, )
29: VAR_008881 (I244T, chain A/C, )
30: VAR_060562 (C253R, chain A/C, )
31: VAR_060563 (I279M, chain A/C, )
32: VAR_060564 (I279T, chain A/C, )
33: VAR_060565 (A280V, chain A/C, )
34: VAR_060566 (S287T, chain A/C, )
35: VAR_060567 (R289C, chain A/C, )
36: VAR_048237 (A295T, chain A/C, )
37: VAR_060569 (L298P, chain A/C, )
38: VAR_060570 (V326I, chain A/C, )
39: VAR_060571 (V336D, chain A/C, )
40: VAR_000593 (I340M, chain A/C, )
41: VAR_060572 (G350D, chain A/C, )
42: VAR_007543 (N526K, chain B/D, )
43: VAR_031328 (S600W, chain B/D, )
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/C
T
9
N
02
UniProt
VAR_000587
P
11
L
SPYA_HUMAN
Polymorphism
34116584
A/C
P
11
L
03
UniProt
VAR_048236
N
22
S
SPYA_HUMAN
Polymorphism
34885252
A/C
N
22
S
04
UniProt
VAR_000588
G
41
R
SPYA_HUMAN
Disease (HP1)
---
A/C
G
41
R
05
UniProt
VAR_010969
G
41
V
SPYA_HUMAN
Disease (HP1)
---
A/C
G
41
V
06
UniProt
VAR_008878
G
82
E
SPYA_HUMAN
Disease (HP1)
---
A/C
G
82
E
07
UniProt
VAR_060548
G
82
R
SPYA_HUMAN
Disease (HP1)
---
A/C
G
82
R
08
UniProt
VAR_060549
W
108
R
SPYA_HUMAN
Disease (HP1)
---
A/C
W
108
R
09
UniProt
VAR_060550
A
112
D
SPYA_HUMAN
Disease (HP1)
---
A/C
A
112
D
10
UniProt
VAR_010971
G
116
R
SPYA_HUMAN
Disease (HP1)
---
A/C
G
116
R
11
UniProt
VAR_000589
F
152
I
SPYA_HUMAN
Disease (HP1)
---
A/C
F
152
I
12
UniProt
VAR_060552
L
153
V
SPYA_HUMAN
Disease (HP1)
---
A/C
L
153
V
13
UniProt
VAR_010972
G
156
R
SPYA_HUMAN
Disease (HP1)
---
A/C
G
156
R
14
UniProt
VAR_060553
S
158
L
SPYA_HUMAN
Disease (HP1)
---
A/C
S
158
L
15
UniProt
VAR_060554
G
161
R
SPYA_HUMAN
Disease (HP1)
---
A/C
G
161
R
16
UniProt
VAR_000590
G
170
R
SPYA_HUMAN
Disease (HP1)
---
A/C
G
170
R
17
UniProt
VAR_060555
C
173
Y
SPYA_HUMAN
Disease (HP1)
---
A/C
C
173
Y
18
UniProt
VAR_010973
D
183
N
SPYA_HUMAN
Disease (HP1)
---
A/C
D
183
N
19
UniProt
VAR_000591
S
187
F
SPYA_HUMAN
Disease (HP1)
---
A/C
S
187
F
20
UniProt
VAR_060556
G
190
R
SPYA_HUMAN
Disease (HP1)
---
A/C
G
190
R
21
UniProt
VAR_060557
M
195
R
SPYA_HUMAN
Disease (HP1)
---
A/C
M
195
R
22
UniProt
VAR_060558
D
201
E
SPYA_HUMAN
Disease (HP1)
---
A/C
D
201
E
23
UniProt
VAR_000592
S
205
P
SPYA_HUMAN
Disease (HP1)
---
A/C
S
205
P
24
UniProt
VAR_060559
S
218
L
SPYA_HUMAN
Disease (HP1)
---
A/C
S
218
L
25
UniProt
VAR_008879
R
233
C
SPYA_HUMAN
Disease (HP1)
---
A/C
R
233
C
26
UniProt
VAR_008880
R
233
H
SPYA_HUMAN
Disease (HP1)
---
A/C
R
233
H
27
UniProt
VAR_060560
R
233
L
SPYA_HUMAN
Disease (HP1)
---
A/C
R
233
L
28
UniProt
VAR_060561
D
243
H
SPYA_HUMAN
Disease (HP1)
---
A/C
D
243
H
29
UniProt
VAR_008881
I
244
T
SPYA_HUMAN
Disease (HP1)
---
A/C
I
244
T
30
UniProt
VAR_060562
C
253
R
SPYA_HUMAN
Disease (HP1)
---
A/C
C
253
R
31
UniProt
VAR_060563
I
279
M
SPYA_HUMAN
Disease (HP1)
---
A/C
I
279
M
32
UniProt
VAR_060564
I
279
T
SPYA_HUMAN
Polymorphism
140992177
A/C
I
279
T
33
UniProt
VAR_060565
A
280
V
SPYA_HUMAN
Polymorphism
73106685
A/C
A
280
V
34
UniProt
VAR_060566
S
287
T
SPYA_HUMAN
Disease (HP1)
---
A/C
S
287
T
35
UniProt
VAR_060567
R
289
C
SPYA_HUMAN
Disease (HP1)
---
A/C
R
289
C
36
UniProt
VAR_048237
A
295
T
SPYA_HUMAN
Polymorphism
13408961
A/C
A
295
T
37
UniProt
VAR_060569
L
298
P
SPYA_HUMAN
Disease (HP1)
---
A/C
L
298
P
38
UniProt
VAR_060570
V
326
I
SPYA_HUMAN
Polymorphism
115057148
A/C
V
326
I
39
UniProt
VAR_060571
V
336
D
SPYA_HUMAN
Disease (HP1)
---
A/C
V
336
D
40
UniProt
VAR_000593
I
340
M
SPYA_HUMAN
Polymorphism
4426527
A/C
I
340
M
41
UniProt
VAR_060572
G
350
D
SPYA_HUMAN
Disease (HP1)
---
A/C
G
350
D
42
UniProt
VAR_007543
N
526
K
PEX5_HUMAN
Disease (PBD2B)
---
B/D
N
526
K
43
UniProt
VAR_031328
S
600
W
PEX5_HUMAN
Disease (PBD2B)
---
B/D
S
600
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 14)
Info
All PROSITE Patterns/Profiles
1: AA_TRANSFER_CLASS_5 (A:200-220,C:200-220)
2: TPR (B:335-368,D:556-589)
3: TPR_REGION (B:335-589,D:335-589)
;
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
2
A:200-220
C:200-220
2
TPR
PS50005
TPR repeat profile.
PEX5_HUMAN
335-368
369-402
488-521
522-555
556-589
10
B:335-368
D:335-368
B:369-402
D:369-402
B:488-521
D:488-521
B:522-555
D:522-555
B:556-589
D:556-589
3
TPR_REGION
PS50293
TPR repeat region circular profile.
PEX5_HUMAN
335-589
2
B:335-589
D:335-589
[
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]
Exons
(0, 0)
Info
All Exons
View:
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3r9ab_ (B:)
1b: SCOP_d3r9ad_ (D:)
2a: SCOP_d3r9aa_ (A:)
2b: SCOP_d3r9ac_ (C:)
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
TPR-like
(83)
Family
:
Tetratricopeptide repeat (TPR)
(47)
Protein domain
:
automated matches
(11)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d3r9ab_
B:
1b
d3r9ad_
D:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
Cystathionine synthase-like
(64)
Protein domain
:
automated matches
(14)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d3r9aa_
A:
2b
d3r9ac_
C:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(3, 10)
Info
all PFAM domains
1a: PFAM_Aminotran_5_3r9aC01 (C:24-376)
1b: PFAM_Aminotran_5_3r9aC02 (C:24-376)
2a: PFAM_TPR_1_3r9aD01 (D:556-589)
2b: PFAM_TPR_1_3r9aD02 (D:556-589)
2c: PFAM_TPR_1_3r9aD03 (D:556-589)
2d: PFAM_TPR_1_3r9aD04 (D:556-589)
2e: PFAM_TPR_1_3r9aD05 (D:556-589)
2f: PFAM_TPR_1_3r9aD06 (D:556-589)
3a: PFAM_TPR_11_3r9aD07 (D:339-400)
3b: PFAM_TPR_11_3r9aD08 (D:339-400)
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Clans
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(
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(
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Organisms
(
)
(
)
Clan
:
PLP_aminotran
(240)
Family
:
Aminotran_5
(20)
Homo sapiens (Human)
(1)
1a
Aminotran_5-3r9aC01
C:24-376
1b
Aminotran_5-3r9aC02
C:24-376
Clan
:
TPR
(230)
Family
:
TPR_1
(18)
Homo sapiens (Human)
(11)
2a
TPR_1-3r9aD01
D:556-589
2b
TPR_1-3r9aD02
D:556-589
2c
TPR_1-3r9aD03
D:556-589
2d
TPR_1-3r9aD04
D:556-589
2e
TPR_1-3r9aD05
D:556-589
2f
TPR_1-3r9aD06
D:556-589
Family
:
TPR_11
(16)
Homo sapiens (Human)
(2)
3a
TPR_11-3r9aD07
D:339-400
3b
TPR_11-3r9aD08
D:339-400
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