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1PZN
Biol. Unit 2
Info
Asym.Unit (272 KB)
Biol.Unit 1 (513 KB)
Biol.Unit 2 (259 KB)
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(1)
Title
:
RAD51 (RADA)
Authors
:
D. S. Shin, J. A. Tainer
Date
:
12 Jul 03 (Deposition) - 09 Sep 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B,C,D,E,F,G (2x)
Biol. Unit 2: A,B,C,D,E,F,G (1x)
Keywords
:
Heptameric Ring; Heptamer; Ring; Oligomer; Rad51 Polymerization Motif; Helix-Hairpin-Helix; Dna Repair; Dna Recombination; Atpase; Homologous Recombination, Recombination
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. S. Shin, L. Pellegrini, D. S. Daniels, B. Yelent, L. Craig, D. Bates, D. S. Yu, M. K. Shivji, C. Hitomi, A. S. Arvai, N. Volkmann, H. Tsuruta, T. L. Blundell, A. R. Venkitaraman, J. A. Tainer
Full-Length Archaeal Rad51 Structure And Mutants: Mechanism For Rad51 Assembly And Control By Brca2
Embo J. V. 22 4566 2003
[
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Hetero Components
(5, 50)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
2a: IMIDAZOLE (IMDa)
2b: IMIDAZOLE (IMDb)
2c: IMIDAZOLE (IMDc)
2d: IMIDAZOLE (IMDd)
2e: IMIDAZOLE (IMDe)
2f: IMIDAZOLE (IMDf)
2g: IMIDAZOLE (IMDg)
2h: IMIDAZOLE (IMDh)
2i: IMIDAZOLE (IMDi)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
9
Ligand/Ion
GLYCEROL
2
IMD
9
Ligand/Ion
IMIDAZOLE
3
MPD
4
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
MSE
21
Mod. Amino Acid
SELENOMETHIONINE
5
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:141 , SER A:142 , GLY A:143 , LYS A:144 , THR A:145 , HOH A:406 , HOH A:421
BINDING SITE FOR RESIDUE SO4 A 350
02
AC2
SOFTWARE
GLU B:139 , PHE B:140 , GLY B:141 , SER B:142 , GLY B:143 , LYS B:144 , THR B:145
BINDING SITE FOR RESIDUE SO4 B 351
03
AC3
SOFTWARE
GLU C:139 , GLY C:141 , SER C:142 , GLY C:143 , LYS C:144 , THR C:145
BINDING SITE FOR RESIDUE SO4 C 352
04
AC4
SOFTWARE
GLU D:139 , GLY D:141 , SER D:142 , GLY D:143 , LYS D:144 , THR D:145
BINDING SITE FOR RESIDUE SO4 D 353
05
AC5
SOFTWARE
GLU E:139 , PHE E:140 , GLY E:141 , SER E:142 , GLY E:143 , LYS E:144 , THR E:145
BINDING SITE FOR RESIDUE SO4 E 354
06
AC6
SOFTWARE
GLU F:139 , PHE F:140 , GLY F:141 , SER F:142 , GLY F:143 , LYS F:144 , THR F:145
BINDING SITE FOR RESIDUE SO4 F 355
07
AC7
SOFTWARE
GLU G:139 , GLY G:141 , SER G:142 , GLY G:143 , LYS G:144 , THR G:145 , HOH G:401
BINDING SITE FOR RESIDUE SO4 G 356
08
AC8
SOFTWARE
ARG A:99 , TYR B:201
BINDING SITE FOR RESIDUE IMD A 357
09
AC9
SOFTWARE
GLY A:321 , ARG A:323 , LYS F:319 , GLY F:320
BINDING SITE FOR RESIDUE IMD A 358
10
BC1
SOFTWARE
ARG A:251 , GLY B:250 , ARG B:251 , GLY B:252 , ALA B:253 , LEU B:254
BINDING SITE FOR RESIDUE IMD B 359
11
BC2
SOFTWARE
LYS B:319 , GLY B:320 , GLY B:321 , ARG E:323
BINDING SITE FOR RESIDUE IMD B 360
12
BC3
SOFTWARE
LYS A:319 , GLY A:320 , GLY F:321 , ARG F:323
BINDING SITE FOR RESIDUE IMD A 361
13
BC4
SOFTWARE
ARG B:99 , TYR C:201 , HOH C:443
BINDING SITE FOR RESIDUE IMD C 362
14
BC5
SOFTWARE
ARG E:99 , TYR F:201 , LYS F:221 , GLU F:224
BINDING SITE FOR RESIDUE IMD F 363
15
BC6
SOFTWARE
TYR A:201 , ARG G:99
BINDING SITE FOR RESIDUE IMD A 364
16
BC7
SOFTWARE
GLY B:321 , ARG B:323 , LYS E:319
BINDING SITE FOR RESIDUE IMD B 365
17
BC8
SOFTWARE
HIS F:199 , ARG F:230
BINDING SITE FOR RESIDUE GOL F 366
18
BC9
SOFTWARE
ARG A:99 , LYS B:198
BINDING SITE FOR RESIDUE GOL B 367
19
CC1
SOFTWARE
ARG C:99 , LYS D:198
BINDING SITE FOR RESIDUE GOL C 368
20
CC2
SOFTWARE
THR D:96 , ALA E:203
BINDING SITE FOR RESIDUE GOL D 369
21
CC3
SOFTWARE
LYS C:198
BINDING SITE FOR RESIDUE GOL C 370
22
CC4
SOFTWARE
ARG D:99 , LYS E:198
BINDING SITE FOR RESIDUE GOL E 371
23
CC5
SOFTWARE
ARG E:99 , LYS F:198
BINDING SITE FOR RESIDUE GOL F 372
24
CC6
SOFTWARE
ARG F:99 , LYS G:198
BINDING SITE FOR RESIDUE GOL F 373
25
CC7
SOFTWARE
LYS A:198
BINDING SITE FOR RESIDUE GOL A 374
26
CC8
SOFTWARE
ALA A:61 , LYS A:263 , ALA A:266 , ASP A:267 , ASN B:207
BINDING SITE FOR RESIDUE MPD B 375
27
CC9
SOFTWARE
ARG D:99 , TYR E:201 , LYS E:221 , GLU E:224
BINDING SITE FOR RESIDUE MPD E 376
28
DC1
SOFTWARE
ARG G:183 , GLN G:187
BINDING SITE FOR RESIDUE MPD G 377
29
DC2
SOFTWARE
GLN G:146 , ILE G:342
BINDING SITE FOR RESIDUE MPD G 378
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 14)
Info
All PROSITE Patterns/Profiles
1: RECA_2 (A:109-285,B:109-285,C:109-285,D:10...)
2: RECA_3 (A:302-349,B:302-349,C:302-349,D:30...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RECA_2
PS50162
RecA family profile 1.
RADA_PYRFU
109-285
7
A:109-285
B:109-285
C:109-285
D:109-285
E:109-285
F:109-285
G:109-285
2
RECA_3
PS50163
RecA family profile 2.
RADA_PYRFU
290-349
7
A:302-349
B:302-349
C:302-349
D:302-349
E:302-349
F:302-349
G:303-349
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1pzna1 (A:35-95)
2a: SCOP_d1pzna2 (A:96-349)
2b: SCOP_d1pznb1 (B:96-349)
2c: SCOP_d1pznc1 (C:96-349)
2d: SCOP_d1pznd1 (D:96-349)
2e: SCOP_d1pzne1 (E:96-349)
2f: SCOP_d1pznf1 (F:96-349)
2g: SCOP_d1pzng1 (G:96-349)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
SAM domain-like
(639)
Superfamily
:
Rad51 N-terminal domain-like
(25)
Family
:
DNA repair protein Rad51, N-terminal domain
(16)
Protein domain
:
DNA repair protein Rad51, N-terminal domain
(16)
Pyrococcus furiosus [TaxId: 2261]
(1)
1a
d1pzna1
A:35-95
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
RecA protein-like (ATPase-domain)
(159)
Protein domain
:
DNA repair protein Rad51, catalytic domain
(18)
Pyrococcus furiosus [TaxId: 2261]
(1)
2a
d1pzna2
A:96-349
2b
d1pznb1
B:96-349
2c
d1pznc1
C:96-349
2d
d1pznd1
D:96-349
2e
d1pzne1
E:96-349
2f
d1pznf1
F:96-349
2g
d1pzng1
G:96-349
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1pznA02 (A:101-349)
1b: CATH_1pznG00 (G:96-349)
1c: CATH_1pznB00 (B:96-349)
1d: CATH_1pznC00 (C:96-349)
1e: CATH_1pznD00 (D:96-349)
1f: CATH_1pznE00 (E:96-349)
1g: CATH_1pznF00 (F:96-349)
2a: CATH_1pznA01 (A:35-100)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Pyrococcus furiosus. Organism_taxid: 2261.
(5)
1a
1pznA02
A:101-349
1b
1pznG00
G:96-349
1c
1pznB00
B:96-349
1d
1pznC00
C:96-349
1e
1pznD00
D:96-349
1f
1pznE00
E:96-349
1g
1pznF00
F:96-349
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
Pyrococcus furiosus. Organism_taxid: 2261.
(2)
2a
1pznA01
A:35-100
[
close CATH info
]
Pfam Domains
(1, 7)
Info
all PFAM domains
1a: PFAM_Rad51_1pznG01 (G:96-349)
1b: PFAM_Rad51_1pznG02 (G:96-349)
1c: PFAM_Rad51_1pznG03 (G:96-349)
1d: PFAM_Rad51_1pznG04 (G:96-349)
1e: PFAM_Rad51_1pznG05 (G:96-349)
1f: PFAM_Rad51_1pznG06 (G:96-349)
1g: PFAM_Rad51_1pznG07 (G:96-349)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Rad51
(10)
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
(1)
1a
Rad51-1pznG01
G:96-349
1b
Rad51-1pznG02
G:96-349
1c
Rad51-1pznG03
G:96-349
1d
Rad51-1pznG04
G:96-349
1e
Rad51-1pznG05
G:96-349
1f
Rad51-1pznG06
G:96-349
1g
Rad51-1pznG07
G:96-349
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Asym.Unit (272 KB)
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