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3BRB
Asym. Unit
Info
Asym.Unit (192 KB)
Biol.Unit 1 (92 KB)
Biol.Unit 2 (94 KB)
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Title
:
CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF THE PROTO-ONCOGENE TYROSINE-PROTEIN KINASE MER IN COMPLEX WITH ADP
Authors
:
J. R. Walker, X. Huang, P. J. Finerty Jr, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics C (Sgc)
Date
:
21 Dec 07 (Deposition) - 22 Jan 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Atp-Binding, Disease Mutation, Glycoprotein, Kinase, Nucleotide- Binding, Phosphorylation, Proto-Oncogene, Receptor, Retinitis Pigmentosa, Sensory Transduction, Transferase, Tyrosine-Protein Kinase, Vision, Structural Genomics, Structural Genomics Consortium, Sgc, Immunoglobulin Domain, Membrane, Phosphoprotein, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Huang, P. Finerty, J. R. Walker, C. Butler-Cole, M. Vedadi, M. Schapira, S. A. Parker, B. E. Turk, D. A. Thompson, S. Dhe-Paganon
Structural Insights Into The Inhibited States Of The Mer Receptor Tyrosine Kinase.
J. Struct. Biol. V. 165 88 2009
[
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: GLYCEROL (GOLa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CL
5
Ligand/Ion
CHLORIDE ION
3
GOL
1
Ligand/Ion
GLYCEROL
4
MG
2
Ligand/Ion
MAGNESIUM ION
[
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Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:211 , ARG A:687 , MET A:798 , ARG B:687
BINDING SITE FOR RESIDUE CL A 4
02
AC2
SOFTWARE
HOH A:37 , LYS A:820
BINDING SITE FOR RESIDUE CL A 5
03
AC3
SOFTWARE
ARG B:584 , LEU B:589
BINDING SITE FOR RESIDUE CL B 6
04
AC4
SOFTWARE
LYS B:820
BINDING SITE FOR RESIDUE CL B 7
05
AC5
SOFTWARE
ARG B:651 , PRO B:672 , ARG B:732
BINDING SITE FOR RESIDUE CL B 8
06
AC6
SOFTWARE
HOH B:238 , HOH B:239 , ASN B:728 , ASP B:741 , ADP B:901
BINDING SITE FOR RESIDUE MG B 9
07
AC7
SOFTWARE
HOH A:20 , HOH A:240 , ASN A:728 , ASP A:741 , ADP A:901
BINDING SITE FOR RESIDUE MG A 10
08
AC8
SOFTWARE
MG A:10 , HOH A:20 , HOH A:21 , HOH A:38 , HOH A:99 , HOH A:240 , LEU A:593 , VAL A:601 , ALA A:617 , LYS A:619 , PRO A:672 , PHE A:673 , MET A:674 , ASP A:678 , ARG A:727 , ASN A:728 , ASP A:741
BINDING SITE FOR RESIDUE ADP A 901
09
AC9
SOFTWARE
MG B:9 , HOH B:65 , HOH B:96 , HOH B:189 , HOH B:235 , HOH B:238 , HOH B:239 , LEU B:593 , VAL B:601 , ALA B:617 , LYS B:619 , PRO B:672 , PHE B:673 , MET B:674 , ASP B:678 , ARG B:727 , ASN B:728 , ASP B:741
BINDING SITE FOR RESIDUE ADP B 901
10
BC1
SOFTWARE
ARG A:818 , LYS A:820 , GLN A:821 , TYR A:830 , THR B:690
BINDING SITE FOR RESIDUE GOL A 3
[
close Site info
]
SAPs(SNPs)/Variants
(4, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_021047 (S661C, chain B, )
2: VAR_041745 (Q662E, chain B, )
3: VAR_041746 (A708S, chain A/B, )
4: VAR_041747 (E823Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021047
S
661
C
MERTK_HUMAN
Disease (RP38)
---
B
S
661
C
2
UniProt
VAR_041745
Q
662
E
MERTK_HUMAN
Polymorphism
56209758
B
Q
662
E
3
UniProt
VAR_041746
A
708
S
MERTK_HUMAN
Unclassified
---
A/B
A
708
S
4
UniProt
VAR_041747
E
823
Q
MERTK_HUMAN
Polymorphism
55924349
A/B
E
823
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:593-619,B:593-619)
2: PROTEIN_KINASE_TYR (A:719-731,B:719-731)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
MERTK_HUMAN
593-619
2
A:593-619
B:593-619
2
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
MERTK_HUMAN
719-731
2
A:719-731
B:719-731
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.23a (A:575-595 | B:575-596)
Exon 1.24 (A:597-621 | B:596-623)
Exon 1.25a (A:625-654 | B:623-654)
Exon 1.29 (A:654-693 (gaps) | B:654-693)
Exon 1.36 (A:694-730 | B:694-730)
Exon 1.38 (A:730-783 (gaps) | B:730-783 (gaps...)
Exon 1.39c (A:784-829 | B:784-829)
Exon 1.45e (A:829-861 | B:829-863)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.22/1.23a
2: Boundary 1.23a/1.24
3: Boundary 1.24/1.25a
4: Boundary 1.25a/1.29
5: Boundary 1.29/1.36
6: Boundary 1.36/1.38
7: Boundary 1.38/1.39c
8: Boundary 1.39c/1.45e
9: Boundary 1.45e/-
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
ENST00000295408
1a
ENSE00001254759
chr2:
112656056-112656373
318
MERTK_HUMAN
1-21
21
0
-
-
1.2b
ENST00000295408
2b
ENSE00001254651
chr2:
112686697-112687117
421
MERTK_HUMAN
21-161
141
0
-
-
1.3
ENST00000295408
3
ENSE00001751676
chr2:
112702537-112702637
101
MERTK_HUMAN
161-195
35
0
-
-
1.4
ENST00000295408
4
ENSE00001658702
chr2:
112704971-112705144
174
MERTK_HUMAN
195-253
59
0
-
-
1.5
ENST00000295408
5
ENSE00001692438
chr2:
112722768-112722854
87
MERTK_HUMAN
253-282
30
0
-
-
1.6
ENST00000295408
6
ENSE00001644343
chr2:
112725714-112725829
116
MERTK_HUMAN
282-320
39
0
-
-
1.7
ENST00000295408
7
ENSE00001710837
chr2:
112732866-112733049
184
MERTK_HUMAN
321-382
62
0
-
-
1.8a
ENST00000295408
8a
ENSE00001610621
chr2:
112740419-112740570
152
MERTK_HUMAN
382-432
51
0
-
-
1.9a
ENST00000295408
9a
ENSE00001685624
chr2:
112751828-112751981
154
MERTK_HUMAN
433-484
52
0
-
-
1.21c
ENST00000295408
21c
ENSE00001786989
chr2:
112754900-112755053
154
MERTK_HUMAN
484-535
52
0
-
-
1.22
ENST00000295408
22
ENSE00001609127
chr2:
112758778-112758863
86
MERTK_HUMAN
535-564
30
0
-
-
1.23a
ENST00000295408
23a
ENSE00001786122
chr2:
112760669-112760764
96
MERTK_HUMAN
564-596
33
2
A:575-595
B:575-596
21
22
1.24
ENST00000295408
24
ENSE00001731139
chr2:
112761481-112761561
81
MERTK_HUMAN
596-623
28
2
A:597-621
B:596-623
25
28
1.25a
ENST00000295408
25a
ENSE00001795827
chr2:
112765960-112766052
93
MERTK_HUMAN
623-654
32
2
A:625-654
B:623-654
30
32
1.29
ENST00000295408
29
ENSE00001693586
chr2:
112767525-112767643
119
MERTK_HUMAN
654-693
40
2
A:654-693 (gaps)
B:654-693
40
40
1.36
ENST00000295408
36
ENSE00001789903
chr2:
112776990-112777099
110
MERTK_HUMAN
694-730
37
2
A:694-730
B:694-730
37
37
1.38
ENST00000295408
38
ENSE00001793083
chr2:
112778999-112779158
160
MERTK_HUMAN
730-783
54
2
A:730-783 (gaps)
B:730-783 (gaps)
54
54
1.39c
ENST00000295408
39c
ENSE00001710351
chr2:
112779835-112779971
137
MERTK_HUMAN
784-829
46
2
A:784-829
B:784-829
46
46
1.45e
ENST00000295408
45e
ENSE00001427300
chr2:
112785928-112787138
1211
MERTK_HUMAN
829-999
171
2
A:829-861
B:829-863
33
35
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3brbB01 (B:575-673)
1b: CATH_3brbA01 (A:575-673)
2a: CATH_3brbA02 (A:674-859)
2b: CATH_3brbB02 (B:674-859)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phosphorylase Kinase; domain 1
(1392)
Homologous Superfamily
:
Phosphorylase Kinase; domain 1
(1392)
Human (Homo sapiens)
(1036)
1a
3brbB01
B:575-673
1b
3brbA01
A:575-673
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
2a
3brbA02
A:674-859
2b
3brbB02
B:674-859
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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