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4IBZ
Asym. Unit
Info
Asym.Unit (284 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (71 KB)
Biol.Unit 3 (70 KB)
Biol.Unit 4 (73 KB)
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(1)
Title
:
HUMAN P53 CORE DOMAIN WITH HOT SPOT MUTATION R273C AND SECOND-SITE SUPPRESSOR MUTATION T284R
Authors
:
A. Eldar, H. Rozenberg, Y. Diskin-Posner, Z. Shakked
Date
:
09 Dec 12 (Deposition) - 14 Aug 13 (Release) - 23 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.92
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Metal-Binding, Loop-Sheet-Helix Motif, Transcription, Activator, Anti-Oncogene, Apoptosis, Cell Cycle, Disease Mutation, Rescue Mutation, Tumor Suppressor, Dna Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Eldar, H. Rozenberg, Y. Diskin-Posner, R. Rohs, Z. Shakked
Structural Studies Of P53 Inactivation By Dna-Contact Mutations And Its Rescue By Suppressor Mutations Via Alternative Protein-Dna Interactions.
Nucleic Acids Res. V. 41 8748 2013
[
close entry info
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Hetero Components
(3, 25)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
EDO
19
Ligand/Ion
1,2-ETHANEDIOL
3
ZN
4
Ligand/Ion
ZINC ION
[
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]
Sites
(25, 25)
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)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:176 , HIS A:179 , CYS A:238 , CYS A:242
BINDING SITE FOR RESIDUE ZN A 301
02
AC2
SOFTWARE
THR A:170 , VAL A:172
BINDING SITE FOR RESIDUE EDO A 302
03
AC3
SOFTWARE
ARG A:158 , ALA A:159 , MET A:160 , ILE A:254 , THR A:256 , HOH A:433 , HOH A:439
BINDING SITE FOR RESIDUE EDO A 303
04
AC4
SOFTWARE
ASP A:186 , ARG A:196 , VAL A:197 , GLU A:198 , ASN A:235 , MET A:237
BINDING SITE FOR RESIDUE EDO A 304
05
AC5
SOFTWARE
THR A:102 , HOH A:555
BINDING SITE FOR RESIDUE EDO A 305
06
AC6
SOFTWARE
CYS B:176 , HIS B:179 , CYS B:238 , CYS B:242
BINDING SITE FOR RESIDUE ZN B 301
07
AC7
SOFTWARE
SER B:260 , SER B:261 , HOH B:529 , ALA D:119 , LYS D:120 , HOH D:435
BINDING SITE FOR RESIDUE EDO B 302
08
AC8
SOFTWARE
ASP B:207 , HOH B:470 , HOH B:506 , LEU D:114 , HIS D:115
BINDING SITE FOR RESIDUE EDO B 303
09
AC9
SOFTWARE
PRO B:190 , PRO B:191 , GLN B:192 , HIS B:193 , ASP B:207 , HIS B:214 , HOH B:456 , HIS D:115
BINDING SITE FOR RESIDUE EDO B 304
10
BC1
SOFTWARE
PHE B:113 , HIS B:115 , GLN B:144 , HOH B:541 , EDO D:302 , EDO D:306
BINDING SITE FOR RESIDUE EDO B 305
11
BC2
SOFTWARE
MET B:160 , LEU B:206 , ASP B:208 , THR B:211 , ARG B:213 , HIS B:214 , SER B:215 , HOH B:503 , HOH B:562
BINDING SITE FOR RESIDUE EDO B 306
12
BC3
SOFTWARE
ARG B:110 , HOH B:505 , EDO D:302 , EDO D:307
BINDING SITE FOR RESIDUE ACT B 307
13
BC4
SOFTWARE
CYS C:176 , HIS C:179 , CYS C:238 , CYS C:242
BINDING SITE FOR RESIDUE ZN C 301
14
BC5
SOFTWARE
PRO C:98 , ARG C:158 , MET C:160 , ILE C:254 , THR C:256 , HOH C:437
BINDING SITE FOR RESIDUE EDO C 302
15
BC6
SOFTWARE
LEU A:114 , HIS A:115 , SER A:116 , ASP C:207 , ARG C:209 , HOH C:496
BINDING SITE FOR RESIDUE EDO C 303
16
BC7
SOFTWARE
ALA A:119 , SER C:261 , GLY C:262 , HOH C:467
BINDING SITE FOR RESIDUE EDO C 304
17
BC8
SOFTWARE
ARG C:209 , ASN C:210
BINDING SITE FOR RESIDUE EDO C 305
18
BC9
SOFTWARE
CYS D:176 , HIS D:179 , CYS D:238 , CYS D:242
BINDING SITE FOR RESIDUE ZN D 301
19
CC1
SOFTWARE
HIS B:115 , TRP B:146 , EDO B:305 , ACT B:307 , PRO D:191 , GLN D:192 , EDO D:307
BINDING SITE FOR RESIDUE EDO D 302
20
CC2
SOFTWARE
LEU D:114 , SER D:116 , CYS D:124 , THR D:125 , TYR D:126 , HOH D:434 , HOH D:527
BINDING SITE FOR RESIDUE EDO D 303
21
CC3
SOFTWARE
SER D:240 , ARG D:248 , CYS D:273
BINDING SITE FOR RESIDUE EDO D 304
22
CC4
SOFTWARE
MET D:160 , LEU D:206 , ASP D:208 , THR D:211 , ARG D:213 , HIS D:214 , SER D:215 , HOH D:442 , HOH D:520
BINDING SITE FOR RESIDUE EDO D 305
23
CC5
SOFTWARE
LEU B:114 , HIS B:115 , EDO B:305 , ASP D:207 , HOH D:432
BINDING SITE FOR RESIDUE EDO D 306
24
CC6
SOFTWARE
TRP B:146 , ACT B:307 , GLU D:180 , PRO D:191 , EDO D:302 , HOH D:526 , HOH D:541
BINDING SITE FOR RESIDUE EDO D 307
25
CC7
SOFTWARE
GLY D:187 , HOH D:450 , HOH D:482
BINDING SITE FOR RESIDUE ACT D 308
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d4ibza_ (A:)
1b: SCOP_d4ibzb_ (B:)
1c: SCOP_d4ibzc_ (C:)
1d: SCOP_d4ibzd_ (D:)
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Classes
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Common fold of diphtheria toxin/transcription factors/cytochrome f
(364)
Superfamily
:
p53-like transcription factors
(153)
Family
:
p53 DNA-binding domain-like
(80)
Protein domain
:
p53 tumor suppressor, DNA-binding domain
(33)
Human (Homo sapiens) [TaxId: 9606]
(32)
1a
d4ibza_
A:
1b
d4ibzb_
B:
1c
d4ibzc_
C:
1d
d4ibzd_
D:
[
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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
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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]
Atom Selection
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Protein
Nucleic
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Sidechain
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (284 KB)
Header - Asym.Unit
Biol.Unit 1 (72 KB)
Header - Biol.Unit 1
Biol.Unit 2 (71 KB)
Header - Biol.Unit 2
Biol.Unit 3 (70 KB)
Header - Biol.Unit 3
Biol.Unit 4 (73 KB)
Header - Biol.Unit 4
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