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1MA9
Asym. Unit
Info
Asym.Unit (138 KB)
Biol.Unit 1 (133 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN VITAMIN D BINDING PROTEIN AND RABBIT MUSCLE ACTIN
Authors
:
C. Verboven, I. Bogaerts, E. Waelkens, A. Rabijns, H. Van Baelen, R. Bouillon, C. De Ranter
Date
:
02 Aug 02 (Deposition) - 04 Feb 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Protein-Protein Complex, Complex Formed In Plasma, Actin Scavenger System, Transport Protein/Contractile Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Verboven, I. Bogaerts, E. Waelkens, A. Rabijns, H. Van Baelen, R. Bouillon, C. De Ranter
Actin-Dbp: The Perfect Structural Fit?
Acta Crystallogr. , Sect. D V. 59 263 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: 4-METHYL-HISTIDINE (HICa)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
HIC
1
Mod. Amino Acid
4-METHYL-HISTIDINE
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ATP B:377 , HOH B:415 , HOH B:493 , HOH B:494 , HOH B:495
BINDING SITE FOR RESIDUE MG B 376
2
AC2
SOFTWARE
GLY B:13 , SER B:14 , GLY B:15 , LEU B:16 , LYS B:18 , GLY B:156 , ASP B:157 , GLY B:158 , VAL B:159 , GLY B:182 , ARG B:210 , LYS B:213 , GLU B:214 , GLY B:301 , GLY B:302 , THR B:303 , MET B:305 , TYR B:306 , LYS B:336 , MG B:376 , HOH B:384 , HOH B:393 , HOH B:399 , HOH B:415 , HOH B:422 , HOH B:441 , HOH B:475 , HOH B:493 , HOH B:494 , HOH B:495
BINDING SITE FOR RESIDUE ATP B 377
[
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_000548 (E416E, chain A, )
2: VAR_000549 (T420T, chain A, )
3: VAR_014120 (R429C, chain A, )
4: VAR_014121 (R429H, chain A, )
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
E
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
(5, 5)
Info
All PROSITE Patterns/Profiles
1: ALBUMIN_2 (-|A:193-378)
2: ACTINS_1 (B:53-63)
3: ACTINS_ACT_LIKE (B:104-116)
4: ALBUMIN_1 (A:166-190)
5: ACTINS_2 (B:356-364)
;
View:
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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
1
-
A:193-378
2
ACTINS_1
PS00406
Actins signature 1.
ACTS_RABIT
55-65
1
B:53-63
3
ACTINS_ACT_LIKE
PS01132
Actins and actin-related proteins signature.
ACTS_RABIT
106-118
1
B:104-116
4
ALBUMIN_1
PS00212
Albumin domain signature.
VTDB_HUMAN
182-206
1
A:166-190
5
ACTINS_2
PS00432
Actins signature 2.
ACTS_RABIT
358-366
1
B:356-364
[
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]
Exons
(12, 12)
Info
All Exons
Exon 1.3a (A:1-4)
Exon 1.4b (A:4-27)
Exon 1.5 (A:27-71)
Exon 1.6b (A:72-142 (gaps))
Exon 1.7 (A:142-186)
Exon 1.8 (A:187-218)
Exon 1.9 (A:218-261)
Exon 1.10 (A:262-329 (gaps))
Exon 1.11 (A:329-372 (gaps))
Exon 1.12a (A:373-405)
Exon 1.13 (A:405-449)
Exon 1.14 (A:450-458)
View:
Select:
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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
A:1-4
4
1.4b
ENST00000273951
4b
ENSE00000969915
chr4:
72635117-72635048
70
VTDB_HUMAN
20-43
24
1
A:4-27
24
1.5
ENST00000273951
5
ENSE00000969916
chr4:
72634150-72634018
133
VTDB_HUMAN
43-87
45
1
A:27-71
45
1.6b
ENST00000273951
6b
ENSE00000969917
chr4:
72631360-72631149
212
VTDB_HUMAN
88-158
71
1
A:72-142 (gaps)
71
1.7
ENST00000273951
7
ENSE00000969918
chr4:
72629653-72629521
133
VTDB_HUMAN
158-202
45
1
A:142-186
45
1.8
ENST00000273951
8
ENSE00000969919
chr4:
72629219-72629125
95
VTDB_HUMAN
203-234
32
1
A:187-218
32
1.9
ENST00000273951
9
ENSE00000969920
chr4:
72623888-72623759
130
VTDB_HUMAN
234-277
44
1
A:218-261
44
1.10
ENST00000273951
10
ENSE00000969921
chr4:
72622631-72622429
203
VTDB_HUMAN
278-345
68
1
A:262-329 (gaps)
68
1.11
ENST00000273951
11
ENSE00000969922
chr4:
72620824-72620695
130
VTDB_HUMAN
345-388
44
1
A:329-372 (gaps)
44
1.12a
ENST00000273951
12a
ENSE00000969923
chr4:
72620225-72620128
98
VTDB_HUMAN
389-421
33
1
A:373-405
33
1.13
ENST00000273951
13
ENSE00001138618
chr4:
72618367-72618235
133
VTDB_HUMAN
421-465
45
1
A:405-449
45
1.14
ENST00000273951
14
ENSE00001178657
chr4:
72611922-72611868
55
VTDB_HUMAN
466-474
9
1
A:450-458
9
1.15f
ENST00000273951
15f
ENSE00002022228
chr4:
72607587-72607410
178
VTDB_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(2, 5)
Info
All SCOP Domains
1a: SCOP_d1ma9a1 (A:1-198)
1b: SCOP_d1ma9a2 (A:199-386)
1c: SCOP_d1ma9a3 (A:387-458)
2a: SCOP_d1ma9b1 (B:5-146)
2b: SCOP_d1ma9b2 (B:147-371)
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)
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)
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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
d1ma9a1
A:1-198
1b
d1ma9a2
A:199-386
1c
d1ma9a3
A:387-458
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
Actin/HSP70
(199)
Protein domain
:
Actin
(69)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(55)
2a
d1ma9b1
B:5-146
2b
d1ma9b2
B:147-371
[
close SCOP info
]
CATH Domains
(4, 9)
Info
all CATH domains
1a: CATH_1ma9B01 (B:6-34,B:71-134,B:337-369)
1b: CATH_1ma9B03 (B:136-181,B:271-332)
2a: CATH_1ma9B04 (B:182-267)
3a: CATH_1ma9A02 (A:124-211)
3b: CATH_1ma9A03 (A:212-299)
3c: CATH_1ma9A01 (A:3-111)
3d: CATH_1ma9A04 (A:315-391)
3e: CATH_1ma9A05 (A:398-457)
4a: CATH_1ma9B02 (B:35-68)
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)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.40, no name defined]
(217)
Human (Homo sapiens)
(36)
1a
1ma9B01
B:6-34,B:71-134,B:337-369
1b
1ma9B03
B:136-181,B:271-332
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Actin; Chain A, domain 4
(156)
Homologous Superfamily
:
Actin; Chain A, domain 4
(155)
Human (Homo sapiens)
(29)
2a
1ma9B04
B:182-267
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)
3a
1ma9A02
A:124-211
3b
1ma9A03
A:212-299
3c
1ma9A01
A:3-111
3d
1ma9A04
A:315-391
3e
1ma9A05
A:398-457
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Actin; Chain A, domain 2
(36)
Homologous Superfamily
:
Actin; Chain A, domain 2
(36)
Human (Homo sapiens)
(7)
4a
1ma9B02
B:35-68
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (138 KB)
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