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1PB8
Asym. Unit
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Asym.Unit (56 KB)
Biol.Unit 1 (52 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-SERINE AT 1.45 ANGSTROMS RESOLUTION
Authors
:
H. Furukawa, E. Gouaux
Date
:
14 May 03 (Deposition) - 24 Jun 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Ligand Binding Receptor; Rat; Nr1, Ligand Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Furukawa, E. Gouaux
Mechanisms Of Activation, Inhibition And Specificity: Crystal Structures Of The Nmda Receptor Nr1 Ligand-Binding Core
Embo J. V. 22 2873 2003
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: D-SERINE (DSNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DSN
1
Ligand/Ion
D-SERINE
[
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]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE A:92 , PRO A:124 , THR A:126 , ARG A:131 , SER A:179 , SER A:180 , VAL A:181 , TRP A:223 , ASP A:224
BINDING SITE FOR RESIDUE DSN A 901
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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
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(9, 9)
Info
All Exons
Exon 1.9 (A:4-7)
Exon 1.10 (A:8-48)
Exon 1.11 (A:56-97)
Exon 1.12 (A:98-152)
Exon 1.13 (A:153-154)
Exon 1.15 (A:155-163)
Exon 1.16 (A:164-216)
Exon 1.17 (A:216-270)
Exon 1.18 (A:270-292)
View:
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All Exon Boundaries
01: Boundary 1.8/1.9
02: Boundary 1.9/1.10
03: Boundary 1.10/1.11
04: Boundary 1.11/1.12
05: Boundary 1.12/1.13
06: Boundary 1.13/1.14
07: Boundary 1.14/1.15
08: Boundary 1.15/1.16
09: Boundary 1.16/1.17
10: Boundary 1.17/1.18
11: Boundary 1.18/1.19
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
1.1
ENSRNOT00000049297
1
ENSRNOE00000310130
chr3:
3480369-3479901
469
NMDZ1_RAT
1-86
86
0
-
-
1.2
ENSRNOT00000049297
2
ENSRNOE00000111277
chr3:
3478540-3478406
135
NMDZ1_RAT
87-131
45
0
-
-
1.3
ENSRNOT00000049297
3
ENSRNOE00000111402
chr3:
3474895-3474719
177
NMDZ1_RAT
132-190
59
0
-
-
1.5
ENSRNOT00000049297
5
ENSRNOE00000111535
chr3:
3471911-3471811
101
NMDZ1_RAT
191-224
34
0
-
-
1.6
ENSRNOT00000049297
6
ENSRNOE00000114140
chr3:
3466978-3466857
122
NMDZ1_RAT
224-265
42
0
-
-
1.7
ENSRNOT00000049297
7
ENSRNOE00000114576
chr3:
3466784-3466610
175
NMDZ1_RAT
265-323
59
0
-
-
1.8
ENSRNOT00000049297
8
ENSRNOE00000111937
chr3:
3465637-3465493
145
NMDZ1_RAT
323-371
49
0
-
-
1.9
ENSRNOT00000049297
9
ENSRNOE00000112066
chr3:
3465395-3465312
84
NMDZ1_RAT
372-399
28
1
A:4-7
4
1.10
ENSRNOT00000049297
10
ENSRNOE00000112201
chr3:
3461058-3460917
142
NMDZ1_RAT
400-447
48
1
A:8-48
41
1.11
ENSRNOT00000049297
11
ENSRNOE00000112339
chr3:
3460834-3460707
128
NMDZ1_RAT
447-489
43
1
A:56-97
42
1.12
ENSRNOT00000049297
12
ENSRNOE00000112471
chr3:
3460461-3460297
165
NMDZ1_RAT
490-544
55
1
A:98-152
55
1.13
ENSRNOT00000049297
13
ENSRNOE00000112596
chr3:
3460222-3460104
119
NMDZ1_RAT
545-584
40
1
A:153-154
2
1.14
ENSRNOT00000049297
14
ENSRNOE00000112738
chr3:
3459988-3459876
113
NMDZ1_RAT
584-622
39
0
-
-
1.15
ENSRNOT00000049297
15
ENSRNOE00000112879
chr3:
3459799-3459651
149
NMDZ1_RAT
622-671
50
1
A:155-163
9
1.16
ENSRNOT00000049297
16
ENSRNOE00000113022
chr3:
3459544-3459387
158
NMDZ1_RAT
672-724
53
1
A:164-216
53
1.17
ENSRNOT00000049297
17
ENSRNOE00000115047
chr3:
3459215-3459054
162
NMDZ1_RAT
724-778
55
1
A:216-270
55
1.18
ENSRNOT00000049297
18
ENSRNOE00000331986
chr3:
3458645-3458536
110
NMDZ1_RAT
778-815
38
1
A:270-292
23
1.19
ENSRNOT00000049297
19
ENSRNOE00000347456
chr3:
3458452-3458307
146
NMDZ1_RAT
815-863
49
0
-
-
1.20
ENSRNOT00000049297
20
ENSRNOE00000118114
chr3:
3457054-3456944
111
NMDZ1_RAT
864-900
37
0
-
-
1.21
ENSRNOT00000049297
21
ENSRNOE00000259023
chr3:
3455031-3453784
1248
NMDZ1_RAT
901-938
38
0
-
-
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1pb8a_ (A:)
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(
)
(
)
Folds
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)
(
)
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)
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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
:
N-methyl-D-aspartate receptor subunit 1
(15)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(14)
1a
d1pb8a_
A:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1pb8A01 (A:4-143,A:252-292)
1b: CATH_1pb8A02 (A:144-251)
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(
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(
)
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)
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)
(
)
Homologous Superfamilies
(
)
(
)
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
1pb8A01
A:4-143,A:252-292
1b
1pb8A02
A:144-251
[
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]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Lig_chan_1pb8A01 (A:155-292)
2a: PFAM_SBP_bac_3_1pb8A02 (A:62-287)
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Clans
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)
(
)
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)
(
)
Organisms
(
)
(
)
Clan
:
Ion_channel
(150)
Family
:
Lig_chan
(109)
Rattus norvegicus (Rat)
(101)
1a
Lig_chan-1pb8A01
A:155-292
Clan
:
PBP
(391)
Family
:
SBP_bac_3
(32)
Rattus norvegicus (Rat)
(17)
2a
SBP_bac_3-1pb8A02
A:62-287
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Chain A
Asymmetric Unit 1
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