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1Z83
Asym. Unit
Info
Asym.Unit (114 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (70 KB)
Biol.Unit 3 (37 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN AK1A IN COMPLEX WITH AP5A
Authors
:
P. Filippakopoulos, G. Bunkoczi, A. Jansson, A. Schreurs, S. Knapp, A. F. Von Delft, M. Sundstrom, Structural Genomics Consortium (Sgc
Date
:
29 Mar 05 (Deposition) - 26 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B (1x)
Biol. Unit 2: B,C (1x)
Biol. Unit 3: C (1x)
Keywords
:
Adenylate Kinase, Humna, Ap5A, Diadenosine Pentaphosphate, Nucleotide Kinase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Filippakopoulos, G. Bunkoczi, A. Jansson, A. Schreurs, S. Knapp, A. Edwards, F. Von Delft, M. Sundstrom
Crystal Structure Of Human Ak1A In Complex With Ap5A
To Be Published
[
close entry info
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: BIS(ADENOSINE)-5'-PENTAPHOSPHATE (AP5a)
1b: BIS(ADENOSINE)-5'-PENTAPHOSPHATE (AP5b)
1c: BIS(ADENOSINE)-5'-PENTAPHOSPHATE (AP5c)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AP5
3
Ligand/Ion
BIS(ADENOSINE)-5'-PENTAPHOSPHATE
2
SO4
3
Ligand/Ion
SULFATE ION
3
ZN
8
Ligand/Ion
ZINC ION
[
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Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
AP5 A:631 , HOH A:703 , HOH A:704 , HOH A:838 , HOH A:845
BINDING SITE FOR RESIDUE ZN A 601
02
AC2
SOFTWARE
AP5 B:632 , HOH B:704 , HOH B:776 , HOH B:805 , HOH B:811
BINDING SITE FOR RESIDUE ZN B 611
03
AC3
SOFTWARE
AP5 C:633 , HOH C:646 , HOH C:647 , HOH C:732 , HOH C:741
BINDING SITE FOR RESIDUE ZN C 621
04
AC4
SOFTWARE
GLU A:26 , HIS A:36 , GLU A:144 , HOH A:840 , HOH A:846
BINDING SITE FOR RESIDUE ZN A 641
05
AC5
SOFTWARE
GLU A:70 , ASP A:74 , GLU B:70 , GLU B:104 , ARG B:108
BINDING SITE FOR RESIDUE ZN B 642
06
AC6
SOFTWARE
GLU B:26 , HIS B:36 , HOH B:806 , HOH B:812 , GLU C:144
BINDING SITE FOR RESIDUE ZN B 643
07
AC7
SOFTWARE
GLU B:144 , GLU C:26 , HIS C:36 , HOH C:733 , HOH C:742
BINDING SITE FOR RESIDUE ZN C 644
08
AC8
SOFTWARE
GLU C:70 , ASP C:74 , ARG C:108
BINDING SITE FOR RESIDUE ZN C 645
09
AC9
SOFTWARE
THR B:35 , LYS B:83 , THR B:86 , SER B:87
BINDING SITE FOR RESIDUE SO4 B 701
10
BC1
SOFTWARE
ARG A:107 , HOH A:858 , ARG B:53
BINDING SITE FOR RESIDUE SO4 A 702
11
BC2
SOFTWARE
ALA A:82 , LYS A:83 , HOH A:872 , SER B:0 , MET B:1 , HOH B:740
BINDING SITE FOR RESIDUE SO4 B 703
12
BC3
SOFTWARE
PRO A:17 , GLY A:18 , SER A:19 , GLY A:20 , LYS A:21 , GLY A:22 , THR A:23 , THR A:39 , GLY A:40 , LEU A:43 , ARG A:44 , MET A:61 , GLN A:65 , LEU A:66 , VAL A:67 , GLY A:94 , TYR A:95 , ARG A:97 , GLN A:101 , ARG A:128 , ARG A:132 , ARG A:138 , ARG A:149 , GLY A:177 , SER A:178 , VAL A:179 , ZN A:601 , HOH A:703 , HOH A:704 , HOH A:707 , HOH A:709 , HOH A:710 , HOH A:720 , HOH A:723 , HOH A:725 , HOH A:732 , HOH A:738 , HOH A:755 , HOH A:783 , HOH A:789 , HOH A:820 , HOH A:838 , HOH A:845
BINDING SITE FOR RESIDUE AP5 A 631
13
BC4
SOFTWARE
GLY B:16 , PRO B:17 , GLY B:18 , SER B:19 , GLY B:20 , LYS B:21 , GLY B:22 , THR B:23 , THR B:39 , GLY B:40 , LEU B:43 , ARG B:44 , MET B:61 , GLN B:65 , LEU B:66 , VAL B:67 , GLY B:94 , TYR B:95 , ARG B:97 , GLN B:101 , ARG B:128 , LEU B:129 , ARG B:132 , ARG B:138 , ARG B:149 , GLY B:177 , VAL B:179 , ZN B:611 , HOH B:704 , HOH B:705 , HOH B:711 , HOH B:726 , HOH B:728 , HOH B:776 , HOH B:778 , HOH B:797 , HOH B:803 , HOH B:805 , HOH B:811 , HOH B:838
BINDING SITE FOR RESIDUE AP5 B 632
14
BC5
SOFTWARE
LYS B:63 , GLY C:16 , PRO C:17 , GLY C:18 , SER C:19 , GLY C:20 , LYS C:21 , GLY C:22 , THR C:23 , THR C:39 , GLY C:40 , LEU C:43 , ARG C:44 , MET C:61 , GLN C:65 , LEU C:66 , VAL C:67 , GLY C:94 , TYR C:95 , ARG C:97 , GLN C:101 , ARG C:128 , ARG C:132 , ARG C:138 , ARG C:149 , GLY C:177 , VAL C:179 , ZN C:621 , HOH C:646 , HOH C:647 , HOH C:649 , HOH C:659 , HOH C:663 , HOH C:672 , HOH C:674 , HOH C:684 , HOH C:688 , HOH C:701 , HOH C:703 , HOH C:710 , HOH C:732
BINDING SITE FOR RESIDUE AP5 C 633
[
close Site info
]
SAPs(SNPs)/Variants
(5, 15)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_055337 (G40R, chain A/B/C, )
2: VAR_055338 (G64R, chain A/B/C, )
3: VAR_034046 (E123Q, chain A/B/C, )
4: VAR_004021 (R128W, chain A/B/C, )
5: VAR_055340 (Y164C, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_055337
G
40
R
KAD1_HUMAN
Disease (HAAKD)
---
A/B/C
G
40
R
2
UniProt
VAR_055338
G
64
R
KAD1_HUMAN
Disease (HAAKD)
---
A/B/C
G
64
R
3
UniProt
VAR_034046
E
123
Q
KAD1_HUMAN
Polymorphism
8192462
A/B/C
E
123
Q
4
UniProt
VAR_004021
R
128
W
KAD1_HUMAN
Disease (HAAKD)
28930974
A/B/C
R
128
W
5
UniProt
VAR_055340
Y
164
C
KAD1_HUMAN
Disease (HAAKD)
---
A/B/C
Y
164
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: ADENYLATE_KINASE (A:90-101,B:90-101,C:90-101)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADENYLATE_KINASE
PS00113
Adenylate kinase signature.
KAD1_HUMAN
90-101
3
A:90-101
B:90-101
C:90-101
[
close PROSITE info
]
Exons
(6, 18)
Info
All Exons
Exon 1.3a (A:1-3 | B:1-3 | C:1-3)
Exon 1.4c (A:3-15 | B:3-15 | C:3-15)
Exon 1.4e (A:15-69 | B:15-69 | C:15-69)
Exon 1.5 (A:70-108 | B:70-108 | C:70-108)
Exon 1.6 (A:109-172 | B:109-172 | C:109-172)
Exon 1.7e (A:173-194 | B:173-194 | C:173-194)
View:
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All Exon Boundaries
1: Boundary 1.1a/1.3a
2: Boundary 1.3a/1.4c
3: Boundary 1.4c/1.4e
4: Boundary 1.4e/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7e
7: Boundary 1.7e/-
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
ENST00000373176
1a
ENSE00001459734
chr9:
130640022-130639902
121
KAD1_HUMAN
-
0
0
-
-
1.3a
ENST00000373176
3a
ENSE00002044723
chr9:
130636928-130636890
39
KAD1_HUMAN
1-3
3
3
A:1-3
B:1-3
C:1-3
3
3
3
1.4c
ENST00000373176
4c
ENSE00001604283
chr9:
130635340-130635305
36
KAD1_HUMAN
3-15
13
3
A:3-15
B:3-15
C:3-15
13
13
13
1.4e
ENST00000373176
4e
ENSE00000729990
chr9:
130635132-130634969
164
KAD1_HUMAN
15-69
55
3
A:15-69
B:15-69
C:15-69
55
55
55
1.5
ENST00000373176
5
ENSE00000729987
chr9:
130634218-130634102
117
KAD1_HUMAN
70-108
39
3
A:70-108
B:70-108
C:70-108
39
39
39
1.6
ENST00000373176
6
ENSE00000729985
chr9:
130630791-130630600
192
KAD1_HUMAN
109-172
64
3
A:109-172
B:109-172
C:109-172
64
64
64
1.7e
ENST00000373176
7e
ENSE00001459722
chr9:
130630355-130628759
1597
KAD1_HUMAN
173-194
22
3
A:173-194
B:173-194
C:173-194
22
22
22
[
close EXON info
]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1z83a_ (A:)
1b: SCOP_d1z83b_ (B:)
1c: SCOP_d1z83c_ (C:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Nucleotide and nucleoside kinases
(231)
Protein domain
:
automated matches
(25)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1z83a_
A:
1b
d1z83b_
B:
1c
d1z83c_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1z83A00 (A:0-194)
1b: CATH_1z83B00 (B:0-194)
1c: CATH_1z83C00 (C:0-194)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
1z83A00
A:0-194
1b
1z83B00
B:0-194
1c
1z83C00
C:0-194
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_ADK_1z83C01 (C:13-169)
1b: PFAM_ADK_1z83C02 (C:13-169)
1c: PFAM_ADK_1z83C03 (C:13-169)
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Clans
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(
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(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
ADK
(22)
Homo sapiens (Human)
(4)
1a
ADK-1z83C01
C:13-169
1b
ADK-1z83C02
C:13-169
1c
ADK-1z83C03
C:13-169
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Asym.Unit (114 KB)
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