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1J7E
Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (76 KB)
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(1)
Title
:
A STRUCTURAL BASIS FOR THE UNIQUE BINDING FEATURES OF THE HUMAN VITAMIN D-BINDING PROTEIN
Authors
:
C. Verboven, A. Rabijns, M. De Maeyer, H. Van Baelen, R. Bouillon, C. De Ranter
Date
:
16 May 01 (Deposition) - 06 Feb 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Vitamin D Binding, Vitamin D3 Analogue, Group-Specific Component, Gc-Globulin, Transport, Ligand Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Verboven, A. Rabijns, M. De Maeyer, H. Van Baelen, R. Bouillon, C. De Ranter
A Structural Basis For The Unique Binding Features Of The Human Vitamin D-Binding Protein.
Nat. Struct. Biol. V. 9 131 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: 3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-... (JYa)
1b: 3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-... (JYb)
2a: OLEIC ACID (OLAa)
2b: OLEIC ACID (OLAb)
2c: OLEIC ACID (OLAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
JY
2
Ligand/Ion
3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-CYCLOHEXYLIDENE)-ETHYLIDENE]-7A-METHYL-OCTAHYDRO-INDEN-1-YL}-PROPYL)-PHENOL
2
OLA
3
Ligand/Ion
OLEIC ACID
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]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:8 , VAL A:12 , GLU A:15 , SER A:28 , LEU A:31 , TYR A:32 , LYS A:35 , LEU A:75 , SER A:76 , SER A:79 , MET A:107 , HOH A:521 , ASP B:364 , THR B:367
BINDING SITE FOR RESIDUE JY A 501
2
AC2
SOFTWARE
GLU B:8 , GLU B:15 , LEU B:27 , SER B:28 , TYR B:32 , PHE B:36 , LEU B:47 , TYR B:68 , SER B:76 , SER B:79 , MET B:107
BINDING SITE FOR RESIDUE JY B 502
3
AC3
SOFTWARE
VAL A:348 , GLU A:350 , PRO A:351 , LYS A:354 , GLU A:379 , PHE A:383 , ASP A:451
BINDING SITE FOR RESIDUE OLA A 502
4
AC4
SOFTWARE
GLU B:379
BINDING SITE FOR RESIDUE OLA B 503
5
AC5
SOFTWARE
ASP A:361 , ALA B:208 , ALA B:209 , TYR B:210 , LYS B:214 , LEU B:444
BINDING SITE FOR RESIDUE OLA B 504
[
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_000548 (D416E, chain A/B, )
2: VAR_000549 (T420T, chain A/B, )
3: VAR_014120 (R429C, chain A/B, )
4: VAR_014121 (R429H, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_000548
D
432
E
VTDB_HUMAN
Polymorphism
7041
A/B
D
416
E
2
UniProt
VAR_000549
K
436
T
VTDB_HUMAN
Polymorphism
4588
A/B
T
420
T
3
UniProt
VAR_014120
R
445
C
VTDB_HUMAN
Polymorphism
---
A/B
R
429
C
4
UniProt
VAR_014121
R
445
H
VTDB_HUMAN
Polymorphism
9016
A/B
R
429
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ALBUMIN_2 (-|A:193-378,B:193-378)
2: ALBUMIN_1 (A:166-190,B:166-190)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALBUMIN_2
PS51438
Albumin domain profile.
VTDB_HUMAN
16-208
209-394
2
-
A:193-378
B:193-378
2
ALBUMIN_1
PS00212
Albumin domain signature.
VTDB_HUMAN
182-206
2
A:166-190
B:166-190
[
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]
Exons
(12, 23)
Info
All Exons
Exon 1.3a (- | B:3-4)
Exon 1.4b (A:7-27 | B:4-27)
Exon 1.5 (A:27-71 (gaps) | B:27-71)
Exon 1.6b (A:72-142 (gaps) | B:72-142 (gaps))
Exon 1.7 (A:142-186 | B:142-186)
Exon 1.8 (A:187-218 | B:187-218)
Exon 1.9 (A:218-261 | B:218-261)
Exon 1.10 (A:262-329 | B:262-329)
Exon 1.11 (A:329-372 | B:329-372)
Exon 1.12a (A:373-405 | B:373-405)
Exon 1.13 (A:405-449 | B:405-449)
Exon 1.14 (A:450-457 | B:450-456)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.3a
02: Boundary 1.3a/1.4b
03: Boundary 1.4b/1.5
04: Boundary 1.5/1.6b
05: Boundary 1.6b/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/1.12a
11: Boundary 1.12a/1.13
12: Boundary 1.13/1.14
13: Boundary 1.14/1.15f
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
1.3a
ENST00000273951
3a
ENSE00001138631
chr4:
72650079-72649678
402
VTDB_HUMAN
1-20
20
1
-
B:3-4
-
2
1.4b
ENST00000273951
4b
ENSE00000969915
chr4:
72635117-72635048
70
VTDB_HUMAN
20-43
24
2
A:7-27
B:4-27
21
24
1.5
ENST00000273951
5
ENSE00000969916
chr4:
72634150-72634018
133
VTDB_HUMAN
43-87
45
2
A:27-71 (gaps)
B:27-71
45
45
1.6b
ENST00000273951
6b
ENSE00000969917
chr4:
72631360-72631149
212
VTDB_HUMAN
88-158
71
2
A:72-142 (gaps)
B:72-142 (gaps)
71
71
1.7
ENST00000273951
7
ENSE00000969918
chr4:
72629653-72629521
133
VTDB_HUMAN
158-202
45
2
A:142-186
B:142-186
45
45
1.8
ENST00000273951
8
ENSE00000969919
chr4:
72629219-72629125
95
VTDB_HUMAN
203-234
32
2
A:187-218
B:187-218
32
32
1.9
ENST00000273951
9
ENSE00000969920
chr4:
72623888-72623759
130
VTDB_HUMAN
234-277
44
2
A:218-261
B:218-261
44
44
1.10
ENST00000273951
10
ENSE00000969921
chr4:
72622631-72622429
203
VTDB_HUMAN
278-345
68
2
A:262-329
B:262-329
68
68
1.11
ENST00000273951
11
ENSE00000969922
chr4:
72620824-72620695
130
VTDB_HUMAN
345-388
44
2
A:329-372
B:329-372
44
44
1.12a
ENST00000273951
12a
ENSE00000969923
chr4:
72620225-72620128
98
VTDB_HUMAN
389-421
33
2
A:373-405
B:373-405
33
33
1.13
ENST00000273951
13
ENSE00001138618
chr4:
72618367-72618235
133
VTDB_HUMAN
421-465
45
2
A:405-449
B:405-449
45
45
1.14
ENST00000273951
14
ENSE00001178657
chr4:
72611922-72611868
55
VTDB_HUMAN
466-474
9
2
A:450-457
B:450-456
8
7
1.15f
ENST00000273951
15f
ENSE00002022228
chr4:
72607587-72607410
178
VTDB_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1j7ea1 (A:7-198)
1b: SCOP_d1j7ea2 (A:199-386)
1c: SCOP_d1j7ea3 (A:387-457)
1d: SCOP_d1j7eb1 (B:3-198)
1e: SCOP_d1j7eb2 (B:199-386)
1f: SCOP_d1j7eb3 (B:387-456)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Serum albumin-like
(99)
Superfamily
:
Serum albumin-like
(99)
Family
:
Serum albumin-like
(75)
Protein domain
:
Vitamin D binding protein
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1j7ea1
A:7-198
1b
d1j7ea2
A:199-386
1c
d1j7ea3
A:387-457
1d
d1j7eb1
B:3-198
1e
d1j7eb2
B:199-386
1f
d1j7eb3
B:387-456
[
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CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_1j7eA02 (A:124-211)
1b: CATH_1j7eB02 (B:124-211)
1c: CATH_1j7eA03 (A:212-299)
1d: CATH_1j7eB03 (B:212-299)
1e: CATH_1j7eA01 (A:7-111)
1f: CATH_1j7eB01 (B:7-111)
1g: CATH_1j7eA04 (A:315-391)
1h: CATH_1j7eB04 (B:315-391)
1i: CATH_1j7eA05 (A:398-457)
1j: CATH_1j7eB05 (B:398-456)
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(
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Serum Albumin; Chain A, Domain 1
(74)
Homologous Superfamily
:
[code=1.10.246.10, no name defined]
(60)
Human (Homo sapiens)
(57)
1a
1j7eA02
A:124-211
1b
1j7eB02
B:124-211
1c
1j7eA03
A:212-299
1d
1j7eB03
B:212-299
1e
1j7eA01
A:7-111
1f
1j7eB01
B:7-111
1g
1j7eA04
A:315-391
1h
1j7eB04
B:315-391
1i
1j7eA05
A:398-457
1j
1j7eB05
B:398-456
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Asym.Unit (154 KB)
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