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1J7E
Biol. Unit 1
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
(1, 1)
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:
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Label:
No.
Name
Count
Type
Full Name
1
JY
-1
Ligand/Ion
3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-CYCLOHEXYLIDENE)-ETHYLIDENE]-7A-METHYL-OCTAHYDRO-INDEN-1-YL}-PROPYL)-PHENOL
2
OLA
1
Ligand/Ion
OLEIC ACID
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC5 (SOFTWARE)
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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
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
3
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, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_000548 (D416E, chain A, )
2: VAR_000549 (T420T, chain A, )
3: VAR_014120 (R429C, chain A, )
4: VAR_014121 (R429H, chain A, )
View:
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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
D
416
E
2
UniProt
VAR_000549
K
436
T
VTDB_HUMAN
Polymorphism
4588
A
T
420
T
3
UniProt
VAR_014120
R
445
C
VTDB_HUMAN
Polymorphism
---
A
R
429
C
4
UniProt
VAR_014121
R
445
H
VTDB_HUMAN
Polymorphism
9016
A
R
429
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: ALBUMIN_2 (A:193-378)
2: ALBUMIN_1 (A:166-190)
;
View:
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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
1
-
A:193-378
-
2
ALBUMIN_1
PS00212
Albumin domain signature.
VTDB_HUMAN
182-206
1
A:166-190
-
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Exons
(0, 0)
Info
All Exons
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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
(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
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)
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Organisms
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)
(
)
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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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)
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Chain A
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (154 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (76 KB)
Header - Biol.Unit 2
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