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1M3D
Biol. Unit 1
Info
Asym.Unit (452 KB)
Biol.Unit 1 (229 KB)
Biol.Unit 2 (226 KB)
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(1)
Title
:
STRUCTURE OF TYPE IV COLLAGEN NC1 DOMAINS
Authors
:
M. Sundaramoorthy, M. Meiyappan, P. Todd, B. G. Hudson
Date
:
27 Jun 02 (Deposition) - 07 Jan 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Basement Membrane, Type Iv Collagen, Nc1 Domain, Network Assembly, 3D Domain Swapping, Br-Mad, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sundaramoorthy, M. Meiyappan, P. Todd, B. G. Hudson
Crystal Structure Of Nc1 Domains. Structural Basis For Type Iv Collagen Assembly In Basement Membranes
J. Biol. Chem. V. 277 31142 2002
[
close entry info
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: BROMIDE ION (BRa)
1aa: BROMIDE ION (BRaa)
1ab: BROMIDE ION (BRab)
1ac: BROMIDE ION (BRac)
1ad: BROMIDE ION (BRad)
1ae: BROMIDE ION (BRae)
1af: BROMIDE ION (BRaf)
1ag: BROMIDE ION (BRag)
1ah: BROMIDE ION (BRah)
1ai: BROMIDE ION (BRai)
1aj: BROMIDE ION (BRaj)
1b: BROMIDE ION (BRb)
1c: BROMIDE ION (BRc)
1d: BROMIDE ION (BRd)
1e: BROMIDE ION (BRe)
1f: BROMIDE ION (BRf)
1g: BROMIDE ION (BRg)
1h: BROMIDE ION (BRh)
1i: BROMIDE ION (BRi)
1j: BROMIDE ION (BRj)
1k: BROMIDE ION (BRk)
1l: BROMIDE ION (BRl)
1m: BROMIDE ION (BRm)
1n: BROMIDE ION (BRn)
1o: BROMIDE ION (BRo)
1p: BROMIDE ION (BRp)
1q: BROMIDE ION (BRq)
1r: BROMIDE ION (BRr)
1s: BROMIDE ION (BRs)
1t: BROMIDE ION (BRt)
1u: BROMIDE ION (BRu)
1v: BROMIDE ION (BRv)
1w: BROMIDE ION (BRw)
1x: BROMIDE ION (BRx)
1y: BROMIDE ION (BRy)
1z: BROMIDE ION (BRz)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
3a: LUTETIUM (III) ION (LUa)
3b: LUTETIUM (III) ION (LUb)
3c: LUTETIUM (III) ION (LUc)
3d: LUTETIUM (III) ION (LUd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BR
-1
Ligand/Ion
BROMIDE ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
LU
-1
Ligand/Ion
LUTETIUM (III) ION
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: CC4 (SOFTWARE)
12: CC5 (SOFTWARE)
13: CC7 (SOFTWARE)
14: CC8 (SOFTWARE)
15: DC3 (SOFTWARE)
16: DC5 (SOFTWARE)
17: DC6 (SOFTWARE)
18: DC7 (SOFTWARE)
19: EC2 (SOFTWARE)
20: EC4 (SOFTWARE)
21: EC5 (SOFTWARE)
22: EC6 (SOFTWARE)
23: EC7 (SOFTWARE)
24: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP C:148 , GLU C:149 , HOH C:3063 , ASP F:148 , HOH F:3127
BINDING SITE FOR RESIDUE LU C 2001
02
AC2
SOFTWARE
HOH B:4078 , ASP C:148 , ASP F:148 , GLU F:149 , HOH F:3067
BINDING SITE FOR RESIDUE LU F 2002
03
AC5
SOFTWARE
ASN A:66 , TYR B:189 , ALA D:186
BINDING SITE FOR RESIDUE BR A 3001
04
AC6
SOFTWARE
ALA A:186 , ASN D:66 , TYR E:189
BINDING SITE FOR RESIDUE BR A 3002
05
AC7
SOFTWARE
ALA E:74 , ARG E:76 , ASP E:78 , GLY E:178
BINDING SITE FOR RESIDUE BR E 3003
06
AC8
SOFTWARE
ARG A:179 , ALA D:74 , ARG D:76 , ASP D:78 , GLY D:178
BINDING SITE FOR RESIDUE BR A 3004
07
AC9
SOFTWARE
ALA A:74 , ARG A:76 , ASP A:78 , GLY A:178 , ARG D:179
BINDING SITE FOR RESIDUE BR A 3005
08
BC2
SOFTWARE
ALA C:73 , ARG C:75 , ASP C:77 , HOH C:3064
BINDING SITE FOR RESIDUE BR C 3007
09
BC7
SOFTWARE
ALA B:74 , ARG B:76 , ASP B:78 , GLY B:178
BINDING SITE FOR RESIDUE BR B 3012
10
BC8
SOFTWARE
HOH B:4010 , ALA F:73 , ARG F:75 , ASP F:77 , HOH F:3053
BINDING SITE FOR RESIDUE BR F 3013
11
CC4
SOFTWARE
TYR A:189 , TYR C:63 , ASN C:65 , TYR C:71 , ALA E:186
BINDING SITE FOR RESIDUE BR C 3018
12
CC5
SOFTWARE
ALA C:184 , ASN E:66 , TYR F:187
BINDING SITE FOR RESIDUE BR C 3019
13
CC7
SOFTWARE
ASN B:66 , TYR C:187 , ALA F:184
BINDING SITE FOR RESIDUE BR B 3021
14
CC8
SOFTWARE
ALA B:186 , TYR D:189 , TYR F:63 , ASN F:65
BINDING SITE FOR RESIDUE BR F 3022
15
DC3
SOFTWARE
ARG B:55
BINDING SITE FOR RESIDUE BR B 3026
16
DC5
SOFTWARE
PHE B:168 , ARG B:216 , HOH B:4074
BINDING SITE FOR RESIDUE BR B 3028
17
DC6
SOFTWARE
GLY C:211 , ILE C:213 , ARG C:214
BINDING SITE FOR RESIDUE BR C 3029
18
DC7
SOFTWARE
GLY D:213 , LEU D:215 , ARG D:216
BINDING SITE FOR RESIDUE BR D 3030
19
EC2
SOFTWARE
GLY B:213 , GLU B:214 , LEU B:215 , ARG B:216
BINDING SITE FOR RESIDUE BR B 3034
20
EC4
SOFTWARE
GLY E:213 , LEU E:215 , ARG E:216
BINDING SITE FOR RESIDUE BR E 3036
21
EC5
SOFTWARE
ALA A:194 , THR A:195 , SER A:208 , HIS A:218 , LEU C:62 , TYR C:72
BINDING SITE FOR RESIDUE GOL A 4001
22
EC6
SOFTWARE
LEU A:63 , PHE A:73 , ALA B:194 , THR B:195 , HIS B:218
BINDING SITE FOR RESIDUE GOL B 4002
23
EC7
SOFTWARE
THR D:195 , HIS D:218 , LEU F:62 , TYR F:72
BINDING SITE FOR RESIDUE GOL D 4003
24
EC8
SOFTWARE
LEU D:63 , PHE D:73 , ALA E:194 , THR E:195 , SER E:208 , HIS E:218
BINDING SITE FOR RESIDUE GOL E 4004
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: NC1_IV (F:4-226)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NC1_IV
PS51403
Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile.
CO4A2_BOVIN
4-227
1
F:4-226
CO4A1_BOVIN
5-229
3
A:5-227
D:5-228
E:5-227
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 24)
Info
All SCOP Domains
1a: SCOP_d1m3da1 (A:5-114)
1b: SCOP_d1m3da2 (A:115-227)
1c: SCOP_d1m3db1 (B:6-114)
1d: SCOP_d1m3db2 (B:115-229)
1e: SCOP_d1m3dc1 (C:5-114)
1f: SCOP_d1m3dc2 (C:115-226)
1g: SCOP_d1m3dd1 (D:4-114)
1h: SCOP_d1m3dd2 (D:115-228)
1i: SCOP_d1m3de1 (E:4-114)
1j: SCOP_d1m3de2 (E:115-227)
1k: SCOP_d1m3df1 (F:4-114)
1l: SCOP_d1m3df2 (F:115-226)
1m: SCOP_d1m3dg1 (G:4-114)
1n: SCOP_d1m3dg2 (G:115-228)
1o: SCOP_d1m3dh1 (H:4-114)
1p: SCOP_d1m3dh2 (H:115-227)
1q: SCOP_d1m3di1 (I:5-114)
1r: SCOP_d1m3di2 (I:115-226)
1s: SCOP_d1m3dj1 (J:5-114)
1t: SCOP_d1m3dj2 (J:115-227)
1u: SCOP_d1m3dk1 (K:6-114)
1v: SCOP_d1m3dk2 (K:115-229)
1w: SCOP_d1m3dl1 (L:5-114)
1x: SCOP_d1m3dl2 (L:115-226)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
C-type lectin-like
(322)
Superfamily
:
C-type lectin-like
(322)
Family
:
Noncollagenous (NC1) domain of collagen IV
(4)
Protein domain
:
Noncollagenous (NC1) domain of collagen IV
(4)
Cow (Bos taurus) [TaxId: 9913]
(3)
1a
d1m3da1
A:5-114
1b
d1m3da2
A:115-227
1c
d1m3db1
B:6-114
1d
d1m3db2
B:115-229
1e
d1m3dc1
C:5-114
1f
d1m3dc2
C:115-226
1g
d1m3dd1
D:4-114
1h
d1m3dd2
D:115-228
1i
d1m3de1
E:4-114
1j
d1m3de2
E:115-227
1k
d1m3df1
F:4-114
1l
d1m3df2
F:115-226
1m
d1m3dg1
G:4-114
1n
d1m3dg2
G:115-228
1o
d1m3dh1
H:4-114
1p
d1m3dh2
H:115-227
1q
d1m3di1
I:5-114
1r
d1m3di2
I:115-226
1s
d1m3dj1
J:5-114
1t
d1m3dj2
J:115-227
1u
d1m3dk1
K:6-114
1v
d1m3dk2
K:115-229
1w
d1m3dl1
L:5-114
1x
d1m3dl2
L:115-226
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1m3dB00 (B:6-229)
1b: CATH_1m3dE00 (E:4-227)
1c: CATH_1m3dH00 (H:4-227)
1d: CATH_1m3dK00 (K:6-229)
1e: CATH_1m3dD00 (D:4-228)
1f: CATH_1m3dG00 (G:4-228)
1g: CATH_1m3dA00 (A:5-227)
1h: CATH_1m3dJ00 (J:5-227)
1i: CATH_1m3dF00 (F:4-226)
1j: CATH_1m3dC00 (C:5-226)
1k: CATH_1m3dI00 (I:5-226)
1l: CATH_1m3dL00 (L:5-226)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Noncollagenous (NC1) domain of collagen IV
(4)
Homologous Superfamily
:
Noncollagenous (NC1) domain of collagen IV
(4)
Cattle (Bos taurus)
(3)
1a
1m3dB00
B:6-229
1b
1m3dE00
E:4-227
1c
1m3dH00
H:4-227
1d
1m3dK00
K:6-229
1e
1m3dD00
D:4-228
1f
1m3dG00
G:4-228
1g
1m3dA00
A:5-227
1h
1m3dJ00
J:5-227
1i
1m3dF00
F:4-226
1j
1m3dC00
C:5-226
1k
1m3dI00
I:5-226
1l
1m3dL00
L:5-226
[
close CATH info
]
Pfam Domains
(1, 24)
Info
all PFAM domains
1a: PFAM_C4_1m3dK01 (K:115-228)
1b: PFAM_C4_1m3dK02 (K:115-228)
1c: PFAM_C4_1m3dK03 (K:115-228)
1d: PFAM_C4_1m3dK04 (K:115-228)
1e: PFAM_C4_1m3dK05 (K:115-228)
1f: PFAM_C4_1m3dK06 (K:115-228)
1g: PFAM_C4_1m3dK07 (K:115-228)
1h: PFAM_C4_1m3dK08 (K:115-228)
1i: PFAM_C4_1m3dK09 (K:115-228)
1j: PFAM_C4_1m3dK10 (K:115-228)
1k: PFAM_C4_1m3dK11 (K:115-228)
1l: PFAM_C4_1m3dK12 (K:115-228)
1m: PFAM_C4_1m3dK13 (K:115-228)
1n: PFAM_C4_1m3dK14 (K:115-228)
1o: PFAM_C4_1m3dK15 (K:115-228)
1p: PFAM_C4_1m3dK16 (K:115-228)
1q: PFAM_C4_1m3dL01 (L:112-226)
1r: PFAM_C4_1m3dL02 (L:112-226)
1s: PFAM_C4_1m3dL03 (L:112-226)
1t: PFAM_C4_1m3dL04 (L:112-226)
1u: PFAM_C4_1m3dL05 (L:112-226)
1v: PFAM_C4_1m3dL06 (L:112-226)
1w: PFAM_C4_1m3dL07 (L:112-226)
1x: PFAM_C4_1m3dL08 (L:112-226)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
C_Lectin
(98)
Family
:
C4
(3)
Bos taurus (Bovine)
(2)
1a
C4-1m3dK01
K:115-228
1b
C4-1m3dK02
K:115-228
1c
C4-1m3dK03
K:115-228
1d
C4-1m3dK04
K:115-228
1e
C4-1m3dK05
K:115-228
1f
C4-1m3dK06
K:115-228
1g
C4-1m3dK07
K:115-228
1h
C4-1m3dK08
K:115-228
1i
C4-1m3dK09
K:115-228
1j
C4-1m3dK10
K:115-228
1k
C4-1m3dK11
K:115-228
1l
C4-1m3dK12
K:115-228
1m
C4-1m3dK13
K:115-228
1n
C4-1m3dK14
K:115-228
1o
C4-1m3dK15
K:115-228
1p
C4-1m3dK16
K:115-228
1q
C4-1m3dL01
L:112-226
1r
C4-1m3dL02
L:112-226
1s
C4-1m3dL03
L:112-226
1t
C4-1m3dL04
L:112-226
1u
C4-1m3dL05
L:112-226
1v
C4-1m3dL06
L:112-226
1w
C4-1m3dL07
L:112-226
1x
C4-1m3dL08
L:112-226
[
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