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1DP7
Asym. Unit
Info
Asym.Unit (28 KB)
Biol.Unit 1 (46 KB)
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(1)
Title
:
COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE
Authors
:
K. S. Gajiwala, H. Chen, F. Cornille, B. P. Roques, W. Reith, B. Mach, S. K. Burley
Date
:
23 Dec 99 (Deposition) - 06 Mar 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : D,P
Biol. Unit 1: D,P (2x)
Keywords
:
Winged Helix, Mhc Class Ii Transcription Factor, Protein- Dna Cocrystal Structure, Novel Mode Of Dna Recognition, Transcription/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. S. Gajiwala, H. Chen, F. Cornille, B. P. Roques, W. Reith, B. Mach, S. K. Burley
Structure Of The Winged-Helix Protein Hrfx1 Reveals A New Mode Of Dna Binding.
Nature V. 403 916 2000
(for further references see the
PDB file header
)
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Hetero Components
(3, 5)
Info
All Hetero Components
1a: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUa)
1b: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BRU
2
Mod. Nucleotide
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
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]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH D:37 , HOH D:43 , THR P:56 , HOH P:563
BINDING SITE FOR RESIDUE EDO P 501
2
AC2
SOFTWARE
VAL P:2 , SER P:49 , VAL P:50 , HOH P:549
BINDING SITE FOR RESIDUE EDO P 502
3
AC3
SOFTWARE
PRO P:18 , THR P:21 , MET P:52 , GLY P:53 , ARG P:55 , HOH P:523
BINDING SITE FOR RESIDUE PEG P 503
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RFX_DBD (P:1-76)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RFX_DBD
PS51526
RFX-type winged-helix DNA-binding domain profile.
RFX1_HUMAN
438-513
1
P:1-76
[
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Exons
(3, 3)
Info
All Exons
Exon 1.9 (P:1-1)
Exon 1.10 (P:2-62)
Exon 1.11 (P:62-76)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.8/1.9
2: Boundary 1.9/1.10
3: Boundary 1.10/1.11
4: Boundary 1.11/1.12
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
1.1
ENST00000254325
1
ENSE00001348294
chr19:
14117097-14116915
183
RFX1_HUMAN
-
0
0
-
-
1.2
ENST00000254325
2
ENSE00001055458
chr19:
14104707-14104337
371
RFX1_HUMAN
1-107
107
0
-
-
1.3
ENST00000254325
3
ENSE00000902153
chr19:
14094407-14094298
110
RFX1_HUMAN
107-143
37
0
-
-
1.4
ENST00000254325
4
ENSE00000902152
chr19:
14094082-14093999
84
RFX1_HUMAN
144-171
28
0
-
-
1.5
ENST00000254325
5
ENSE00000902151
chr19:
14093040-14092933
108
RFX1_HUMAN
172-207
36
0
-
-
1.6
ENST00000254325
6
ENSE00000902150
chr19:
14091501-14091385
117
RFX1_HUMAN
208-246
39
0
-
-
1.7
ENST00000254325
7
ENSE00000902149
chr19:
14090354-14090259
96
RFX1_HUMAN
247-278
32
0
-
-
1.8
ENST00000254325
8
ENSE00000902148
chr19:
14088898-14088804
95
RFX1_HUMAN
279-310
32
0
-
-
1.9
ENST00000254325
9
ENSE00000902147
chr19:
14083939-14083555
385
RFX1_HUMAN
310-438
129
1
P:1-1
1
1.10
ENST00000254325
10
ENSE00000902146
chr19:
14080987-14080806
182
RFX1_HUMAN
439-499
61
1
P:2-62
61
1.11
ENST00000254325
11
ENSE00000902145
chr19:
14079706-14079587
120
RFX1_HUMAN
499-539
41
1
P:62-76
15
1.12
ENST00000254325
12
ENSE00000902144
chr19:
14079492-14079377
116
RFX1_HUMAN
539-578
40
0
-
-
1.13
ENST00000254325
13
ENSE00000902143
chr19:
14077563-14077445
119
RFX1_HUMAN
578-617
40
0
-
-
1.14
ENST00000254325
14
ENSE00000902142
chr19:
14077342-14077233
110
RFX1_HUMAN
618-654
37
0
-
-
1.15
ENST00000254325
15
ENSE00000902141
chr19:
14076589-14076438
152
RFX1_HUMAN
654-705
52
0
-
-
1.16
ENST00000254325
16
ENSE00000902140
chr19:
14076358-14076261
98
RFX1_HUMAN
705-737
33
0
-
-
1.17
ENST00000254325
17
ENSE00000902139
chr19:
14074819-14074670
150
RFX1_HUMAN
738-787
50
0
-
-
1.18
ENST00000254325
18
ENSE00000902138
chr19:
14074558-14074350
209
RFX1_HUMAN
788-857
70
0
-
-
1.19
ENST00000254325
19
ENSE00001794399
chr19:
14074087-14073934
154
RFX1_HUMAN
857-908
52
0
-
-
1.20
ENST00000254325
20
ENSE00000902136
chr19:
14073851-14073806
46
RFX1_HUMAN
909-924
16
0
-
-
1.21
ENST00000254325
21
ENSE00001385967
chr19:
14073676-14072353
1324
RFX1_HUMAN
924-979
56
0
-
-
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1dp7p_ (P:)
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(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Winged helix DNA-binding domain
(576)
Family
:
P4 origin-binding domain-like
(2)
Protein domain
:
Class II MHC transcription factor RFX1
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1dp7p_
P:
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1dp7P00 (P:1-76)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
[unclassified]
(77)
1a
1dp7P00
P:1-76
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
(currently selected atoms:
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Protein
Nucleic
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Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain D
Chain P
Asymmetric Unit 1
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