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3Q4U
Asym. Unit
Info
Asym.Unit (435 KB)
Biol.Unit 1 (215 KB)
Biol.Unit 2 (217 KB)
Biol.Unit 3 (218 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ACVR1 KINASE DOMAIN IN COMPLEX WITH LDN-193189
Authors
:
A. Chaikuad, C. Sanvitale, C. D. O. Cooper, P. Mahajan, N. Daga, K. Petri I. Alfano, O. Gileadi, O. Fedorov, C. K. Allerston, T. Krojer, M. Vollm Delft, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, C. Bountra, A. Bull Structural Genomics Consortium (Sgc)
Date
:
24 Dec 10 (Deposition) - 09 Feb 11 (Release) - 18 Jun 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.82
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: C,D (1x)
Keywords
:
Structural Genomics Consortium, Sgc, Protein Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. E. Sanvitale, G. Kerr, A. Chaikuad, M. C. Ramel, A. H. Mohedas, S. Reichert, Y. Wang, J. T. Triffitt, G. D. Cuny, P. B. Yu, C. S. Hill, A. N. Bullock
A New Class Of Small Molecule Inhibitor Of Bmp Signaling.
Plos One V. 8 62721 2013
[
close entry info
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Hetero Components
(3, 30)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
2a: CITRATE ANION (FLCa)
2b: CITRATE ANION (FLCb)
2c: CITRATE ANION (FLCc)
2d: CITRATE ANION (FLCd)
2e: CITRATE ANION (FLCe)
2f: CITRATE ANION (FLCf)
2g: CITRATE ANION (FLCg)
2h: CITRATE ANION (FLCh)
2i: CITRATE ANION (FLCi)
2j: CITRATE ANION (FLCj)
2k: CITRATE ANION (FLCk)
2l: CITRATE ANION (FLCl)
3a: 4-[6-(4-PIPERAZIN-1-YLPHENYL)PYRAZ... (LDNa)
3b: 4-[6-(4-PIPERAZIN-1-YLPHENYL)PYRAZ... (LDNb)
3c: 4-[6-(4-PIPERAZIN-1-YLPHENYL)PYRAZ... (LDNc)
3d: 4-[6-(4-PIPERAZIN-1-YLPHENYL)PYRAZ... (LDNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
14
Ligand/Ion
1,2-ETHANEDIOL
2
FLC
12
Ligand/Ion
CITRATE ANION
3
LDN
4
Ligand/Ion
4-[6-(4-PIPERAZIN-1-YLPHENYL)PYRAZOLO[1,5-A]PYRIMIDIN-3-YL]QUINOLINE
[
close Hetero Component info
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Sites
(30, 30)
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)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:214 , VAL A:222 , ALA A:233 , LEU A:263 , THR A:283 , HIS A:284 , TYR A:285 , HIS A:286 , GLU A:287 , GLY A:289 , ASP A:293 , LYS A:340 , ASN A:341 , LEU A:343 , HOH A:555 , HOH A:836
BINDING SITE FOR RESIDUE LDN A 3
02
AC2
SOFTWARE
ASP A:207 , THR A:209 , SER A:226 , TRP A:227 , GLN A:228 , HOH A:564 , VAL C:419
BINDING SITE FOR RESIDUE EDO A 1
03
AC3
SOFTWARE
THR A:271 , SER A:276 , GLN A:278 , HOH A:1113 , LDN C:4
BINDING SITE FOR RESIDUE EDO A 2
04
AC4
SOFTWARE
EDO A:4 , TYR A:294 , THR A:299 , LEU A:300 , ASP A:301 , SER A:304
BINDING SITE FOR RESIDUE EDO A 500
05
AC5
SOFTWARE
THR A:299 , EDO A:500
BINDING SITE FOR RESIDUE EDO A 4
06
AC6
SOFTWARE
ARG A:380 , ASP A:438 , HOH A:929
BINDING SITE FOR RESIDUE EDO A 5
07
AC7
SOFTWARE
HOH A:163 , HIS A:284 , TYR A:285 , HIS A:286 , GLU A:287 , LYS A:345 , LYS A:346 , FLC A:502 , HOH A:1127
BINDING SITE FOR RESIDUE FLC A 501
08
AC8
SOFTWARE
HOH A:119 , HIS A:259 , GLU A:260 , ILE A:262 , LEU A:263 , GLY A:264 , HIS A:284 , HIS A:286 , LYS A:345 , FLC A:501 , HOH A:1128 , HOH A:1129
BINDING SITE FOR RESIDUE FLC A 502
09
AC9
SOFTWARE
VAL B:214 , VAL B:222 , ALA B:233 , LEU B:263 , THR B:283 , HIS B:284 , TYR B:285 , HIS B:286 , GLU B:287 , GLY B:289 , LYS B:340 , ASN B:341 , LEU B:343 , HOH B:564 , HOH B:833 , HOH B:972
BINDING SITE FOR RESIDUE LDN B 1
10
BC1
SOFTWARE
ILE B:262 , LEU B:263 , GLY B:264 , HIS B:284 , HIS B:286
BINDING SITE FOR RESIDUE EDO B 7
11
BC2
SOFTWARE
TYR B:294 , THR B:299 , LEU B:300 , ASP B:301 , SER B:304
BINDING SITE FOR RESIDUE EDO B 8
12
BC3
SOFTWARE
HIS B:284 , TYR B:285 , HIS B:286 , GLU B:287 , LYS B:345 , LYS B:346 , HOH B:971
BINDING SITE FOR RESIDUE FLC B 5
13
BC4
SOFTWARE
HIS B:318 , LEU B:489 , LYS B:492 , HOH B:552
BINDING SITE FOR RESIDUE FLC B 6
14
BC5
SOFTWARE
ILE B:321 , LYS B:400 , THR B:487 , ALA B:488 , LEU B:489 , HOH B:514 , HOH B:565 , HOH B:979 , HOH B:1133 , ASN D:481 , SER D:483
BINDING SITE FOR RESIDUE FLC B 500
15
BC6
SOFTWARE
LYS B:338 , LYS B:340 , THR B:378 , ARG B:380 , ASN B:437 , ASP B:438 , PRO B:439 , HOH B:555 , HOH B:984
BINDING SITE FOR RESIDUE FLC B 501
16
BC7
SOFTWARE
EDO A:2 , ARG A:273 , SER A:276 , HOH C:59 , VAL C:222 , ALA C:233 , LEU C:263 , THR C:283 , HIS C:284 , TYR C:285 , HIS C:286 , GLU C:287 , GLY C:289 , ASP C:293 , LYS C:340 , ASN C:341 , LEU C:343 , HOH C:537 , HOH C:846
BINDING SITE FOR RESIDUE LDN C 4
17
BC8
SOFTWARE
LYS C:243 , PHE C:246 , ARG C:247 , GLU C:250 , HOH C:521 , HOH D:35 , ASN D:372
BINDING SITE FOR RESIDUE EDO C 9
18
BC9
SOFTWARE
MET C:360 , SER C:362 , GLN C:367
BINDING SITE FOR RESIDUE EDO C 10
19
CC1
SOFTWARE
ASP C:269 , THR C:271 , GLN C:278 , TRP C:280
BINDING SITE FOR RESIDUE EDO C 11
20
CC2
SOFTWARE
FLC C:12 , HOH C:93 , HOH C:165 , HIS C:284 , TYR C:285 , HIS C:286 , GLU C:287 , LYS C:345 , LYS C:346
BINDING SITE FOR RESIDUE FLC C 3
21
CC3
SOFTWARE
HOH C:143 , LYS C:338 , LYS C:340 , ARG C:380 , ASP C:438 , PRO C:439 , HOH C:624 , HOH C:1108
BINDING SITE FOR RESIDUE FLC C 500
22
CC4
SOFTWARE
FLC C:3 , HOH C:155 , ARG C:258 , HIS C:259 , GLU C:260 , ILE C:262 , GLY C:264 , HIS C:284 , HIS C:286 , LYS C:345 , CYS C:351 , HOH C:1083
BINDING SITE FOR RESIDUE FLC C 12
23
CC5
SOFTWARE
VAL D:214 , VAL D:222 , ALA D:233 , LEU D:263 , THR D:283 , HIS D:284 , TYR D:285 , HIS D:286 , GLU D:287 , GLY D:289 , ASP D:293 , LYS D:340 , ASN D:341 , LEU D:343 , HOH D:556 , HOH D:847
BINDING SITE FOR RESIDUE LDN D 2
24
CC6
SOFTWARE
THR D:299 , LEU D:300 , ASP D:301 , VAL D:419
BINDING SITE FOR RESIDUE EDO D 6
25
CC7
SOFTWARE
PHE D:431 , ASP D:433 , GLN D:453 , ARG D:454 , ASN D:456 , HOH D:551 , HOH D:562 , HOH D:1111
BINDING SITE FOR RESIDUE EDO D 12
26
CC8
SOFTWARE
HOH D:30 , ARG D:380 , ASN D:437 , ASP D:438 , PRO D:439 , HOH D:1064
BINDING SITE FOR RESIDUE EDO D 13
27
CC9
SOFTWARE
TRP D:227 , GLN D:228 , GLU D:230
BINDING SITE FOR RESIDUE EDO D 14
28
DC1
SOFTWARE
HIS D:284 , TYR D:285 , HIS D:286 , GLU D:287 , LYS D:345 , LYS D:346 , HOH D:501 , HOH D:521 , HOH D:574 , HOH D:619
BINDING SITE FOR RESIDUE FLC D 9
29
DC2
SOFTWARE
HIS D:259 , GLU D:260 , ILE D:262 , GLY D:264 , HIS D:284 , HIS D:286 , LYS D:345 , HOH D:619
BINDING SITE FOR RESIDUE FLC D 10
30
DC3
SOFTWARE
SER B:483 , ALA B:484 , HOH D:52 , LYS D:400 , THR D:487 , ALA D:488 , LEU D:489 , HOH D:1067 , HOH D:1152
BINDING SITE FOR RESIDUE FLC D 11
[
close Site info
]
SAPs(SNPs)/Variants
(8, 31)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_058419 (R202I, chain A/B/D, )
2: VAR_028444 (R206H, chain A/B/C/D, )
3: VAR_058420 (D207E, chain A/B/C/D, )
4: VAR_058421 (G328E, chain A/B/C/D, )
5: VAR_058422 (G328R, chain A/B/C/D, )
6: VAR_058423 (G328W, chain A/B/C/D, )
7: VAR_058424 (G356D, chain A/B/C/D, )
8: VAR_058425 (R375P, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_058419
R
202
I
ACVR1_HUMAN
Disease (FOP)
---
A/B/D
R
202
I
2
UniProt
VAR_028444
R
206
H
ACVR1_HUMAN
Disease (FOP)
---
A/B/C/D
R
206
H
3
UniProt
VAR_058420
Q
207
E
ACVR1_HUMAN
Disease (FOP)
---
A/B/C/D
D
207
E
4
UniProt
VAR_058421
G
328
E
ACVR1_HUMAN
Disease (FOP)
---
A/B/C/D
G
328
E
5
UniProt
VAR_058422
G
328
R
ACVR1_HUMAN
Disease (FOP)
---
A/B/C/D
G
328
R
6
UniProt
VAR_058423
G
328
W
ACVR1_HUMAN
Disease (FOP)
---
A/B/C/D
G
328
W
7
UniProt
VAR_058424
G
356
D
ACVR1_HUMAN
Disease (FOP)
---
A/B/C/D
G
356
D
8
UniProt
VAR_058425
R
375
P
ACVR1_HUMAN
Disease (FOP)
---
A/B/C/D
R
375
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:214-235,B:214-235,C:214-235,D:21...)
2: PROTEIN_KINASE_ST (A:332-344,B:332-344,C:332-344,D:33...)
;
View:
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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.
ACVR1_HUMAN
214-235
4
A:214-235
B:214-235
C:214-235
D:214-235
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
ACVR1_HUMAN
332-344
4
A:332-344
B:332-344
C:332-344
D:332-344
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
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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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3q4ua_ (A:)
1b: SCOP_d3q4ub_ (B:)
1c: SCOP_d3q4uc_ (C:)
1d: SCOP_d3q4ud_ (D:)
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Classes
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(
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Protein kinase-like (PK-like)
(2589)
Superfamily
:
Protein kinase-like (PK-like)
(2589)
Family
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
automated matches
(542)
Human (Homo sapiens) [TaxId: 9606]
(452)
1a
d3q4ua_
A:
1b
d3q4ub_
B:
1c
d3q4uc_
C:
1d
d3q4ud_
D:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Pkinase_3q4uD01 (D:208-495)
1b: PFAM_Pkinase_3q4uD02 (D:208-495)
1c: PFAM_Pkinase_3q4uD03 (D:208-495)
1d: PFAM_Pkinase_3q4uD04 (D:208-495)
2a: PFAM_TGF_beta_GS_3q4uD05 (D:201-206)
2b: PFAM_TGF_beta_GS_3q4uD06 (D:201-206)
2c: PFAM_TGF_beta_GS_3q4uD07 (D:201-206)
2d: PFAM_TGF_beta_GS_3q4uD08 (D:201-206)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-3q4uD01
D:208-495
1b
Pkinase-3q4uD02
D:208-495
1c
Pkinase-3q4uD03
D:208-495
1d
Pkinase-3q4uD04
D:208-495
Clan
:
no clan defined [family: TGF_beta_GS]
(12)
Family
:
TGF_beta_GS
(12)
Homo sapiens (Human)
(12)
2a
TGF_beta_GS-3q4uD05
D:201-206
2b
TGF_beta_GS-3q4uD06
D:201-206
2c
TGF_beta_GS-3q4uD07
D:201-206
2d
TGF_beta_GS-3q4uD08
D:201-206
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