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3KJ4
Biol. Unit 1
Info
Asym.Unit (235 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (114 KB)
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(1)
Title
:
STRUCTURE OF RAT NOGO RECEPTOR BOUND TO 1D9 ANTAGONIST ANTIBODY
Authors
:
L. F. Silvian
Date
:
02 Nov 09 (Deposition) - 22 Sep 10 (Release) - 27 Oct 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,H,L
Biol. Unit 1: A,H,L (1x)
Biol. Unit 2: B,C,D (1x)
Keywords
:
Nogo Receptor Antagonist Antibody, Lrr, Cell Membrane, Disulfide Bond, Glycoprotein, Gpi-Anchor, Leucine-Rich Repeat, Lipoprotein, Membrane, Receptor, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
P. H. Weinreb, D. Wen, F. Qian, C. P. Wildes, E. A. Garber, L. Walus, M. Y. Jung, J. Wang, J. K. Relton, J. Amatucci, R. Wang, F. Porreca, L. Silvian, W. Meier, R. B. Pepinsky, D. H. Lee
Resolution Of Disulfide Heterogeneity In Nogo Receptor 1 Fusion Proteins By Molecular Engineering.
Biotechnol Appl Biochem V. 57 31 2010
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: ALPHA-D-MANNOSE (MANa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
3b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
3c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
3d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
2
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC8 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:57 , SER A:58 , ARG A:81 , ASN A:82 , NDG A:314
BINDING SITE FOR RESIDUE NDG A 313
2
AC2
SOFTWARE
NDG A:313 , MAN H:303
BINDING SITE FOR RESIDUE NDG A 314
3
AC3
SOFTWARE
NDG A:314
BINDING SITE FOR RESIDUE MAN H 303
4
AC6
SOFTWARE
HIS A:133 , ASN A:179
BINDING SITE FOR RESIDUE NAG A 315
5
AC8
SOFTWARE
TYR H:102 , TRP H:106
BINDING SITE FOR RESIDUE ZN H 221
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: LRR (A:58-79,A:82-103,A:106-128,A:131-1...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LRR
PS51450
Leucine-rich repeat profile.
RTN4R_RAT
58-79
82-103
106-128
131-152
155-176
179-200
203-224
227-248
8
A:58-79
-
A:82-103
-
A:106-128
-
A:131-152
-
A:155-176
-
A:179-200
-
A:203-224
-
A:227-248
-
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Exons
(0, 0)
Info
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3kj4b1 (B:1-112)
1b: SCOP_d3kj4l1 (L:1-112)
2a: SCOP_d3kj4b2 (B:113-219)
2b: SCOP_d3kj4l2 (L:113-219)
3a: SCOP_d3kj4a_ (A:)
3b: SCOP_d3kj4d_ (D:)
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)
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(
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)
(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d3kj4b1
B:1-112
1b
d3kj4l1
L:1-112
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d3kj4b2
B:113-219
2b
d3kj4l2
L:113-219
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(112)
Superfamily
:
L domain-like
(93)
Family
:
Ngr ectodomain-like
(21)
Protein domain
:
automated matches
(3)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
3a
d3kj4a_
A:
3b
d3kj4d_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_LRR_8_3kj4D01 (D:203-261)
1b: PFAM_LRR_8_3kj4D02 (D:203-261)
1c: PFAM_LRR_8_3kj4D03 (D:203-261)
1d: PFAM_LRR_8_3kj4D04 (D:203-261)
1e: PFAM_LRR_8_3kj4D05 (D:203-261)
1f: PFAM_LRR_8_3kj4D06 (D:203-261)
1g: PFAM_LRR_8_3kj4D07 (D:203-261)
1h: PFAM_LRR_8_3kj4D08 (D:203-261)
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Clan
:
LRR
(77)
Family
:
LRR_8
(41)
Rattus norvegicus (Rat)
(1)
1a
LRR_8-3kj4D01
D:203-261
1b
LRR_8-3kj4D02
D:203-261
1c
LRR_8-3kj4D03
D:203-261
1d
LRR_8-3kj4D04
D:203-261
1e
LRR_8-3kj4D05
D:203-261
1f
LRR_8-3kj4D06
D:203-261
1g
LRR_8-3kj4D07
D:203-261
1h
LRR_8-3kj4D08
D:203-261
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (235 KB)
Header - Asym.Unit
Biol.Unit 1 (114 KB)
Header - Biol.Unit 1
Biol.Unit 2 (114 KB)
Header - Biol.Unit 2
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