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1YAE
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (47 KB)
Biol.Unit 2 (47 KB)
Biol.Unit 3 (46 KB)
Biol.Unit 4 (47 KB)
Biol.Unit 5 (47 KB)
Biol.Unit 6 (42 KB)
Biol.Unit 7 (89 KB)
Biol.Unit 8 (88 KB)
Biol.Unit 9 (88 KB)
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(1)
Title
:
STRUCTURE OF THE KAINATE RECEPTOR SUBUNIT GLUR6 AGONIST BINDING DOMAIN COMPLEXED WITH DOMOIC ACID
Authors
:
M. H. Nanao, T. Green, Y. Stern-Bach, S. F. Heinemann, S. Choe
Date
:
17 Dec 04 (Deposition) - 01 Feb 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.11
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: B,D (1x)
Biol. Unit 8: A (2x)
Biol. Unit 9: C,E (1x)
Keywords
:
Kainate Receptor, Glutamate Receptor, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. H. Nanao, T. Green, Y. Stern-Bach, S. F. Heinemann, S. Choe
Structure Of The Kainate Receptor Subunit Glur6 Agonist-Binding Domain Complexed With Domoic Acid.
Proc. Natl. Acad. Sci. Usa V. 102 1708 2005
[
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Hetero Components
(3, 17)
Info
All Hetero Components
1a: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)... (DOQa)
1b: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)... (DOQb)
1c: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)... (DOQc)
1d: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)... (DOQd)
1e: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)... (DOQe)
1f: (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)... (DOQf)
2a: ALPHA-L-FUCOSE (FUCa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DOQ
6
Ligand/Ion
(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
2
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
3
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
FUC A:2 , ASN A:423 , THR A:425 , HOH A:1115 , HOH A:1116
BINDING SITE FOR RESIDUE NAG A 1
02
AC2
SOFTWARE
NAG A:1 , ASP A:426
BINDING SITE FOR RESIDUE FUC A 2
03
AC3
SOFTWARE
HOH B:64 , ASN B:423 , THR B:425
BINDING SITE FOR RESIDUE NAG B 1201
04
AC4
SOFTWARE
ARG B:543 , ASN B:751
BINDING SITE FOR RESIDUE NAG B 1202
05
AC5
SOFTWARE
HOH C:69 , HOH C:70 , ASN C:423 , THR C:425
BINDING SITE FOR RESIDUE NAG C 1301
06
AC6
SOFTWARE
ARG C:543 , ASN C:751
BINDING SITE FOR RESIDUE NAG C 1302
07
AC7
SOFTWARE
ASN D:423 , THR D:425
BINDING SITE FOR RESIDUE NAG D 1401
08
AC8
SOFTWARE
ARG D:543 , ASN D:751
BINDING SITE FOR RESIDUE NAG D 1402
09
AC9
SOFTWARE
HOH E:65 , ASN E:423 , THR E:425
BINDING SITE FOR RESIDUE NAG E 1501
10
BC1
SOFTWARE
HOH E:59 , ARG E:543 , ASN E:751
BINDING SITE FOR RESIDUE NAG E 1502
11
BC2
SOFTWARE
ASN F:423 , THR F:425
BINDING SITE FOR RESIDUE NAG F 1601
12
BC3
SOFTWARE
GLU A:440 , LYS A:487 , TYR A:488 , GLY A:489 , PRO A:516 , ALA A:518 , ARG A:523 , GLU A:686 , GLY A:688 , ALA A:689 , THR A:690 , GLU A:738 , HOH A:1104
BINDING SITE FOR RESIDUE DOQ A 1103
13
BC4
SOFTWARE
HOH B:10 , GLU B:440 , LYS B:487 , TYR B:488 , GLY B:489 , PRO B:516 , ALA B:518 , ARG B:523 , VAL B:685 , GLU B:686 , GLY B:688 , ALA B:689 , THR B:690 , ASN B:721 , GLU B:738
BINDING SITE FOR RESIDUE DOQ B 1203
14
BC5
SOFTWARE
LYS C:487 , TYR C:488 , GLY C:489 , ALA C:490 , PRO C:516 , ALA C:518 , ARG C:523 , VAL C:685 , GLU C:686 , ALA C:689 , THR C:690 , GLU C:738
BINDING SITE FOR RESIDUE DOQ C 1303
15
BC6
SOFTWARE
GLU D:440 , LYS D:487 , TYR D:488 , GLY D:489 , PRO D:516 , ALA D:518 , ARG D:523 , GLU D:686 , GLY D:688 , ALA D:689 , THR D:690 , ASN D:721 , GLU D:738
BINDING SITE FOR RESIDUE DOQ D 1403
16
BC7
SOFTWARE
GLU E:440 , LYS E:487 , TYR E:488 , GLY E:489 , PRO E:516 , ALA E:518 , ARG E:523 , GLU E:686 , ALA E:689 , THR E:690 , GLU E:738
BINDING SITE FOR RESIDUE DOQ E 1503
17
BC8
SOFTWARE
GLU F:440 , LYS F:487 , TYR F:488 , GLY F:489 , PRO F:516 , ALA F:518 , ARG F:523 , GLU F:686 , ALA F:689 , THR F:690 , ASN F:721 , GLU F:738
BINDING SITE FOR RESIDUE DOQ F 1603
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d1yaea1 (A:421-544,A:668-804)
1b: SCOP_d1yaeb1 (B:423-544,B:668-804)
1c: SCOP_d1yaec1 (C:423-544,C:669-802)
1d: SCOP_d1yaed1 (D:423-544,D:668-804)
1e: SCOP_d1yaee1 (E:423-544,E:668-801)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
Glutamate receptor ligand binding core
(127)
Norway rat (Rattus norvegicus), GluR6 [TaxId: 10116]
(3)
1a
d1yaea1
A:421-544,A:668-804
1b
d1yaeb1
B:423-544,B:668-804
1c
d1yaec1
C:423-544,C:669-802
1d
d1yaed1
D:423-544,D:668-804
1e
d1yaee1
E:423-544,E:668-801
[
close SCOP info
]
CATH Domains
(1, 11)
Info
all CATH domains
1a: CATH_1yaeF01 (F:431-536,F:763-800)
1b: CATH_1yaeB02 (B:537-761)
1c: CATH_1yaeE01 (E:423-536,E:762-801)
1d: CATH_1yaeE02 (E:537-761)
1e: CATH_1yaeA02 (A:537-761)
1f: CATH_1yaeC02 (C:537-761)
1g: CATH_1yaeD02 (D:537-761)
1h: CATH_1yaeC01 (C:423-536,C:762-802)
1i: CATH_1yaeB01 (B:423-536,B:762-804)
1j: CATH_1yaeD01 (D:423-536,D:762-804)
1k: CATH_1yaeA01 (A:421-536,A:762-804)
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(
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(
)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
Norway rat (Rattus norvegicus)
(84)
1a
1yaeF01
F:431-536,F:763-800
1b
1yaeB02
B:537-761
1c
1yaeE01
E:423-536,E:762-801
1d
1yaeE02
E:537-761
1e
1yaeA02
A:537-761
1f
1yaeC02
C:537-761
1g
1yaeD02
D:537-761
1h
1yaeC01
C:423-536,C:762-802
1i
1yaeB01
B:423-536,B:762-804
1j
1yaeD01
D:423-536,D:762-804
1k
1yaeA01
A:421-536,A:762-804
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Lig_chan_1yaeF01 (F:680-800)
1b: PFAM_Lig_chan_1yaeF02 (F:680-800)
1c: PFAM_Lig_chan_1yaeF03 (F:680-800)
1d: PFAM_Lig_chan_1yaeF04 (F:680-800)
1e: PFAM_Lig_chan_1yaeF05 (F:680-800)
1f: PFAM_Lig_chan_1yaeF06 (F:680-800)
2a: PFAM_Lig_chan_Glu_bd_1yaeF07 (F:442-506)
2b: PFAM_Lig_chan_Glu_bd_1yaeF08 (F:442-506)
2c: PFAM_Lig_chan_Glu_bd_1yaeF09 (F:442-506)
2d: PFAM_Lig_chan_Glu_bd_1yaeF10 (F:442-506)
2e: PFAM_Lig_chan_Glu_bd_1yaeF11 (F:442-506)
2f: PFAM_Lig_chan_Glu_bd_1yaeF12 (F:442-506)
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Clans
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)
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)
(
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(
)
(
)
Clan
:
Ion_channel
(150)
Family
:
Lig_chan
(109)
Rattus norvegicus (Rat)
(101)
1a
Lig_chan-1yaeF01
F:680-800
1b
Lig_chan-1yaeF02
F:680-800
1c
Lig_chan-1yaeF03
F:680-800
1d
Lig_chan-1yaeF04
F:680-800
1e
Lig_chan-1yaeF05
F:680-800
1f
Lig_chan-1yaeF06
F:680-800
Clan
:
PBP
(391)
Family
:
Lig_chan-Glu_bd
(91)
Rattus norvegicus (Rat)
(86)
2a
Lig_chan-Glu_bd-1yaeF07
F:442-506
2b
Lig_chan-Glu_bd-1yaeF08
F:442-506
2c
Lig_chan-Glu_bd-1yaeF09
F:442-506
2d
Lig_chan-Glu_bd-1yaeF10
F:442-506
2e
Lig_chan-Glu_bd-1yaeF11
F:442-506
2f
Lig_chan-Glu_bd-1yaeF12
F:442-506
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Asym.Unit (261 KB)
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Biol.Unit 3 (46 KB)
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