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1YAE
Biol. Unit 8
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:
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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, 6)
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:
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Label:
No.
Name
Count
Type
Full Name
1
DOQ
2
Ligand/Ion
(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
2
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
FUC A:2 , ASN A:423 , THR A:425 , HOH A:1115 , HOH A:1116
BINDING SITE FOR RESIDUE NAG A 1
2
AC2
SOFTWARE
NAG A:1 , ASP A:426
BINDING SITE FOR RESIDUE FUC A 2
3
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
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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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
(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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Protein Domains
(
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(
)
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
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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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)
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
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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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Organisms
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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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