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1NPE
Asym. Unit
Info
Asym.Unit (76 KB)
Biol.Unit 1 (71 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NIDOGEN/LAMININ COMPLEX
Authors
:
J. Takagi, Y. T. Yang, J. -H. Liu, J. -H. Wang, T. A. Springer
Date
:
17 Jan 03 (Deposition) - 12 Aug 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glycoprotein, Basement Membrane, Beta-Propeller, Egf-Like, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Takagi, Y. T. Yang, J. -H. Liu, J. -H. Wang, T. A. Springer
Complex Between Nidogen And Laminin Fragments Reveals A Paradigmatic Beta-Propeller Interface
Nature V. 424 969 2003
(for further references see the
PDB file header
)
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Hetero Components
(1, 6)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
6
Ligand/Ion
CADMIUM ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:3 , HOH A:23 , HOH A:25 , SER A:1010 , ASP A:1013 , VAL A:1034
BINDING SITE FOR RESIDUE CD A 5001
2
AC2
SOFTWARE
HIS A:1064 , ASP A:1066 , THR A:1068 , HOH B:89 , GLU B:831 , SER B:862
BINDING SITE FOR RESIDUE CD B 5002
3
AC3
SOFTWARE
HOH A:94 , HOH A:108 , HIS A:1101
BINDING SITE FOR RESIDUE CD A 5003
4
AC4
SOFTWARE
HOH A:84 , HIS A:1160 , HIS B:759
BINDING SITE FOR RESIDUE CD B 5004
5
AC5
SOFTWARE
HOH A:102 , HIS A:944 , GLU B:754
BINDING SITE FOR RESIDUE CD A 5005
6
AC6
SOFTWARE
HOH B:105 , HOH B:106 , HIS B:875
BINDING SITE FOR RESIDUE CD B 5006
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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
(4, 11)
Info
All PROSITE Patterns/Profiles
1: EGF_LAM_2 (-|-|-|-|-|B:738-792|B:793-848|B:84...)
2: EGF_1 (-|-|-|-|-|B:870-881|-|-)
3: EGF_LAM_1 (-|-|-|-|-|B:757-793|B:814-849|B:87...)
4: LDLRB (A:960-1002|A:1003-1045|A:1046-1090...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_LAM_2
PS50027
Laminin-type EGF-like (LE) domain profile.
LAMC1_MOUSE
284-329
340-395
396-442
443-492
722-770
771-825
826-881
882-932
933-980
981-1028
3
-
-
-
-
-
B:738-792
B:793-848
B:849-899
-
-
2
EGF_1
PS00022
EGF-like domain signature 1.
LAMC1_MOUSE
303-314
414-425
461-472
688-699
738-749
903-914
952-963
999-1010
1
-
-
-
-
-
B:870-881
-
-
3
EGF_LAM_1
PS01248
Laminin-type EGF-like (LE) domain signature.
LAMC1_MOUSE
365-398
414-445
461-495
688-722
738-773
790-826
847-882
903-935
952-983
999-1032
3
-
-
-
-
-
B:757-793
B:814-849
B:870-899
-
-
4
LDLRB
PS51120
LDL-receptor class B (LDLRB) repeat profile.
NID1_MOUSE
988-1030
1031-1073
1074-1118
1119-1160
4
A:960-1002
A:1003-1045
A:1046-1090
A:1091-1132
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1npea_ (A:)
2a: SCOP_d1npeb1 (B:736-792)
2b: SCOP_d1npeb2 (B:793-848)
2c: SCOP_d1npeb3 (B:849-899)
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)
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Folds
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
6-bladed beta-propeller
(327)
Superfamily
:
YWTD domain
(3)
Family
:
YWTD domain
(3)
Protein domain
:
Nidogen
(1)
Mouse (Mus musculus) [TaxId: 10090]
(1)
1a
d1npea_
A:
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
Laminin-type module
(3)
Protein domain
:
Laminin gamma1 chain
(3)
Mouse (Mus musculus) [TaxId: 10090]
(3)
2a
d1npeb1
B:736-792
2b
d1npeb2
B:793-848
2c
d1npeb3
B:849-899
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1npeA00 (A:913-1175)
2a: CATH_1npeB01 (B:738-790)
2b: CATH_1npeB03 (B:847-899)
2c: CATH_1npeB02 (B:791-846)
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)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
TolB, C-terminal domain
(42)
House mouse (Mus musculus)
(1)
1a
1npeA00
A:913-1175
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
House mouse (Mus musculus)
(18)
2a
1npeB01
B:738-790
2b
1npeB03
B:847-899
2c
1npeB02
B:791-846
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close CATH info
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Ldl_recept_b_1npeA01 (A:1046-1088)
1b: PFAM_Ldl_recept_b_1npeA02 (A:1046-1088)
1c: PFAM_Ldl_recept_b_1npeA03 (A:1046-1088)
2a: PFAM_Laminin_EGF_1npeB01 (B:849-897)
2b: PFAM_Laminin_EGF_1npeB02 (B:849-897)
2c: PFAM_Laminin_EGF_1npeB03 (B:849-897)
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Clans
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)
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
Ldl_recept_b
(3)
Mus musculus (Mouse)
(1)
1a
Ldl_recept_b-1npeA01
A:1046-1088
1b
Ldl_recept_b-1npeA02
A:1046-1088
1c
Ldl_recept_b-1npeA03
A:1046-1088
Clan
:
EGF
(60)
Family
:
Laminin_EGF
(4)
Mus musculus (Mouse)
(4)
2a
Laminin_EGF-1npeB01
B:849-897
2b
Laminin_EGF-1npeB02
B:849-897
2c
Laminin_EGF-1npeB03
B:849-897
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Nucleic
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Asymmetric Unit 1
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Asym.Unit (76 KB)
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