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3KQ4
Biol. Unit 1
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Asym.Unit (900 KB)
Biol.Unit 1 (300 KB)
Biol.Unit 2 (301 KB)
Biol.Unit 3 (302 KB)
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(1)
Title
:
STRUCTURE OF INTRINSIC FACTOR-COBALAMIN BOUND TO ITS RECEPTOR CUBILIN
Authors
:
C. B. F. Andersen, M. Madsen, S. K. Moestrup, G. R. Andersen
Date
:
17 Nov 09 (Deposition) - 09 Mar 10 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Protein-Protein Complex, Cobalt, Cobalt Transport, Disease Mutation, Disulfide Bond, Glycoprotein, Secreted, Transport, Cholesterol Metabolism, Cobalamin, Egf-Like Domain, Endocytosis, Endosome, Lipid Metabolism, Lysosome, Membrane, Protein Transport, Receptor, Steroid Metabolism, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. B. Andersen, M. Madsen, T. Storm, S. K. Moestrup, G. R. Andersen
Structural Basis For Receptor Recognition Of Vitamin-B(12)-Intrinsic Factor Complexes.
Nature V. 464 445 2010
[
close entry info
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Hetero Components
(4, 20)
Info
All Hetero Components
1a: COBALAMIN (B12a)
1b: COBALAMIN (B12b)
1c: COBALAMIN (B12c)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
2d: BETA-D-MANNOSE (BMAd)
2e: BETA-D-MANNOSE (BMAe)
2f: BETA-D-MANNOSE (BMAf)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
3g: CALCIUM ION (CAg)
3h: CALCIUM ION (CAh)
3i: CALCIUM ION (CAi)
3j: CALCIUM ION (CAj)
3k: CALCIUM ION (CAk)
3l: CALCIUM ION (CAl)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
4g: ALPHA-D-MANNOSE (MANg)
4h: ALPHA-D-MANNOSE (MANh)
4i: ALPHA-D-MANNOSE (MANi)
4j: ALPHA-D-MANNOSE (MANj)
4k: ALPHA-D-MANNOSE (MANk)
4l: ALPHA-D-MANNOSE (MANl)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
5ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
5ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
5ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
5ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
5af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
5ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
5ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
5ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
5aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
5ak: N-ACETYL-D-GLUCOSAMINE (NAGak)
5al: N-ACETYL-D-GLUCOSAMINE (NAGal)
5am: N-ACETYL-D-GLUCOSAMINE (NAGam)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
5n: N-ACETYL-D-GLUCOSAMINE (NAGn)
5o: N-ACETYL-D-GLUCOSAMINE (NAGo)
5p: N-ACETYL-D-GLUCOSAMINE (NAGp)
5q: N-ACETYL-D-GLUCOSAMINE (NAGq)
5r: N-ACETYL-D-GLUCOSAMINE (NAGr)
5s: N-ACETYL-D-GLUCOSAMINE (NAGs)
5t: N-ACETYL-D-GLUCOSAMINE (NAGt)
5u: N-ACETYL-D-GLUCOSAMINE (NAGu)
5v: N-ACETYL-D-GLUCOSAMINE (NAGv)
5w: N-ACETYL-D-GLUCOSAMINE (NAGw)
5x: N-ACETYL-D-GLUCOSAMINE (NAGx)
5y: N-ACETYL-D-GLUCOSAMINE (NAGy)
5z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B12
1
Ligand/Ion
COBALAMIN
2
BMA
2
Ligand/Ion
BETA-D-MANNOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:311 , VAL A:335 , SER A:336 , VAL A:337 , GLU A:349
BINDING SITE FOR RESIDUE NAG A 2001
02
AC2
SOFTWARE
ASN A:413 , PHE A:414 , THR A:415 , NAG A:2003
BINDING SITE FOR RESIDUE NAG A 2002
03
AC3
SOFTWARE
GLN A:321 , NAG A:2002 , BMA A:2004
BINDING SITE FOR RESIDUE NAG A 2003
04
AC4
SOFTWARE
NAG A:2003 , MAN A:2005 , MAN A:2006
BINDING SITE FOR RESIDUE BMA A 2004
05
AC5
SOFTWARE
BMA A:2004
BINDING SITE FOR RESIDUE MAN A 2005
06
AC6
SOFTWARE
BMA A:2004
BINDING SITE FOR RESIDUE MAN A 2006
07
AC7
SOFTWARE
GLY A:90 , HIS A:91 , SER A:130 , TYR A:133 , ASP A:171 , ASP A:222 , TYR A:224 , SER A:225 , LEU A:228 , GLN A:270 , THR A:364 , SER A:365 , TRP A:366 , GLY A:367 , VAL A:369 , VAL A:370 , TRP A:386 , PHE A:388 , LEU A:395 , ASN A:396 , GLU A:397 , GLY A:398 , TYR A:417
BINDING SITE FOR RESIDUE B12 A 2007
08
AC8
SOFTWARE
ASN B:984
BINDING SITE FOR RESIDUE NAG B 2001
09
AC9
SOFTWARE
PRO B:1065 , THR B:1091 , ASN B:1092 , NAG B:2003
BINDING SITE FOR RESIDUE NAG B 2002
10
BC1
SOFTWARE
NAG B:2002 , BMA B:2004 , MAN B:2006
BINDING SITE FOR RESIDUE NAG B 2003
11
BC2
SOFTWARE
NAG B:2003 , MAN B:2005 , MAN B:2006
BINDING SITE FOR RESIDUE BMA B 2004
12
BC3
SOFTWARE
BMA B:2004
BINDING SITE FOR RESIDUE MAN B 2005
13
BC4
SOFTWARE
NAG B:2003 , BMA B:2004
BINDING SITE FOR RESIDUE MAN B 2006
14
BC5
SOFTWARE
ASN B:1168
BINDING SITE FOR RESIDUE NAG B 2007
15
BC6
SOFTWARE
ASN B:1217
BINDING SITE FOR RESIDUE NAG B 2008
16
BC7
SOFTWARE
ASN B:1285 , THR B:1313
BINDING SITE FOR RESIDUE NAG B 2009
17
BC8
SOFTWARE
ASN B:1280 , ASN B:1307 , GLN B:1367 , LEU B:1369 , NAG B:2011
BINDING SITE FOR RESIDUE NAG B 2010
18
BC9
SOFTWARE
GLN B:1367 , NAG B:2010
BINDING SITE FOR RESIDUE NAG B 2011
19
CC1
SOFTWARE
ASN B:1319 , SER B:1360
BINDING SITE FOR RESIDUE NAG B 2012
20
CC2
SOFTWARE
ASN B:1332
BINDING SITE FOR RESIDUE NAG B 2013
21
CC3
SOFTWARE
GLU B:980 , ASP B:988 , ASP B:1027 , ASP B:1029 , LEU B:1030
BINDING SITE FOR RESIDUE CA B 2014
22
CC4
SOFTWARE
GLU B:1096 , ASP B:1105 , ASP B:1146 , ILE B:1148 , ASP B:1149
BINDING SITE FOR RESIDUE CA B 2015
23
CC5
SOFTWARE
GLU B:1213 , ASP B:1221 , ASP B:1262 , GLY B:1264 , GLN B:1265 , GLN B:1266
BINDING SITE FOR RESIDUE CA B 2016
24
CC6
SOFTWARE
GLU B:1328 , ASP B:1336 , ASP B:1373 , VAL B:1375
BINDING SITE FOR RESIDUE CA B 2017
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_022743 (S46L, chain A, )
2: VAR_048753 (G65R, chain A, )
3: VAR_022744 (N255S, chain A, )
4: VAR_047446 (L969V, chain B, )
5: VAR_025287 (Y1032H, chain B, )
6: VAR_025288 (P1297L, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_022743
S
46
L
IF_HUMAN
Disease (IFD)
---
A
S
46
L
2
UniProt
VAR_048753
G
65
R
IF_HUMAN
Polymorphism
11825834
A
G
65
R
3
UniProt
VAR_022744
N
255
S
IF_HUMAN
Polymorphism
35867471
A
N
255
S
4
UniProt
VAR_047446
L
969
V
CUBN_HUMAN
Polymorphism
11254354
B
L
969
V
5
UniProt
VAR_025287
Y
1032
H
CUBN_HUMAN
Polymorphism
1801227
B
Y
1032
H
6
UniProt
VAR_025288
P
1297
L
CUBN_HUMAN
Disease (RH-MGA1)
28939699
B
P
1297
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 5)
Info
All PROSITE Patterns/Profiles
1: COBALAMIN_BINDING (A:169-182)
2: CUB ()
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COBALAMIN_BINDING
PS00468
Eukaryotic cobalamin-binding proteins signature.
IF_HUMAN
169-182
1
A:169-182
-
-
2
CUB
PS01180
CUB domain profile.
CUBN_HUMAN
590-702
474-586
708-816
932-1042
816-928
1048-1161
1165-1277
1278-1389
1391-1506
1510-1619
1620-1734
1738-1850
1852-1963
1978-2091
2092-2213
2217-2334
2336-2448
2452-2565
2570-2687
2689-2801
2805-2919
3037-3150
2920-3035
3157-3274
3395-3507
3278-3393
3511-3623
4
-
-
-
B:932-1042
-
-
-
B:1048-1161
-
-
B:1165-1277
-
-
B:1278-1388
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 15)
Info
all PFAM domains
1a: PFAM_Cobalamin_bind_3kq4E01 (E:25-313)
1b: PFAM_Cobalamin_bind_3kq4E02 (E:25-313)
1c: PFAM_Cobalamin_bind_3kq4E03 (E:25-313)
2a: PFAM_CUB_3kq4F01 (F:1278-1386)
2b: PFAM_CUB_3kq4F02 (F:1278-1386)
2c: PFAM_CUB_3kq4F03 (F:1278-1386)
2d: PFAM_CUB_3kq4F04 (F:1278-1386)
2e: PFAM_CUB_3kq4F05 (F:1278-1386)
2f: PFAM_CUB_3kq4F06 (F:1278-1386)
2g: PFAM_CUB_3kq4F07 (F:1278-1386)
2h: PFAM_CUB_3kq4F08 (F:1278-1386)
2i: PFAM_CUB_3kq4F09 (F:1278-1386)
2j: PFAM_CUB_3kq4F10 (F:1278-1386)
2k: PFAM_CUB_3kq4F11 (F:1278-1386)
2l: PFAM_CUB_3kq4F12 (F:1278-1386)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
Cobalamin_bind
(3)
Homo sapiens (Human)
(2)
1a
Cobalamin_bind-3kq4E01
E:25-313
1b
Cobalamin_bind-3kq4E02
E:25-313
1c
Cobalamin_bind-3kq4E03
E:25-313
Clan
:
CUB
(11)
Family
:
CUB
(11)
Homo sapiens (Human)
(8)
2a
CUB-3kq4F01
F:1278-1386
2b
CUB-3kq4F02
F:1278-1386
2c
CUB-3kq4F03
F:1278-1386
2d
CUB-3kq4F04
F:1278-1386
2e
CUB-3kq4F05
F:1278-1386
2f
CUB-3kq4F06
F:1278-1386
2g
CUB-3kq4F07
F:1278-1386
2h
CUB-3kq4F08
F:1278-1386
2i
CUB-3kq4F09
F:1278-1386
2j
CUB-3kq4F10
F:1278-1386
2k
CUB-3kq4F11
F:1278-1386
2l
CUB-3kq4F12
F:1278-1386
[
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]
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