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3GQC
Asym. Unit
Info
Asym.Unit (323 KB)
Biol.Unit 1 (84 KB)
Biol.Unit 2 (82 KB)
Biol.Unit 3 (81 KB)
Biol.Unit 4 (81 KB)
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(1)
Title
:
STRUCTURE OF HUMAN REV1-DNA-DNTP TERNARY COMPLEX
Authors
:
M. K. Swan, A. K. Aggarwal
Date
:
24 Mar 09 (Deposition) - 19 May 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,E,F (1x)
Biol. Unit 2: B,G,H (1x)
Biol. Unit 3: C,I,J (1x)
Biol. Unit 4: D,K,L (1x)
Keywords
:
Protein-Dna Complex, Dna Damage, Dna Repair, Dna Synthesis, Dna- Binding, Magnesium, Metal-Binding, Nucleotidyltransferase, Nucleus, Transferase, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. K. Swan, R. E. Johnson, L. Prakash, S. Prakash, A. K. Aggarwal
Structure Of The Human Rev1-Dna-Dntp Ternary Complex.
J. Mol. Biol. V. 390 699 2009
[
close entry info
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Hetero Components
(3, 21)
Info
All Hetero Components
1a: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPa)
1b: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPb)
1c: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPc)
1d: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPd)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
2b: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCb)
2c: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCc)
2d: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DCP
4
Ligand/Ion
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2
DOC
4
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
MG
13
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:89 , MG A:201 , MG A:202 , ARG A:357 , ASP A:423 , MET A:424 , ASP A:425 , CYS A:426 , PHE A:427 , PHE A:428 , ALA A:509 , SER A:510 , TYR A:513 , ARG A:516 , ASN A:522 , ASP A:570 , LYS A:625
BINDING SITE FOR RESIDUE DCP A 101
02
AC2
SOFTWARE
MG B:203 , ARG B:357 , ASP B:423 , MET B:424 , CYS B:426 , PHE B:427 , PHE B:428 , ALA B:509 , SER B:510 , TYR B:513 , ARG B:516 , ASN B:522 , ASP B:570 , LYS B:625
BINDING SITE FOR RESIDUE DCP B 101
03
AC3
SOFTWARE
HOH C:73 , HOH C:87 , MG C:205 , MG C:206 , ARG C:357 , ASP C:423 , MET C:424 , ASP C:425 , CYS C:426 , PHE C:427 , PHE C:428 , ALA C:509 , SER C:510 , TYR C:513 , ARG C:516 , ASN C:522 , ASP C:570 , LYS C:625 , DOC I:12
BINDING SITE FOR RESIDUE DCP C 101
04
AC4
SOFTWARE
MG D:207 , MG D:208 , ARG D:357 , ASP D:423 , MET D:424 , ASP D:425 , CYS D:426 , PHE D:427 , PHE D:428 , ALA D:509 , SER D:510 , TYR D:513 , ARG D:516 , ASN D:522 , ASP D:570 , LYS D:625
BINDING SITE FOR RESIDUE DCP D 101
05
AC5
SOFTWARE
DCP A:101 , ASP A:423 , MET A:424 , ASP A:570
BINDING SITE FOR RESIDUE MG A 201
06
AC6
SOFTWARE
DCP A:101 , SER A:568 , ASP A:570 , GLU A:571 , DOC E:12
BINDING SITE FOR RESIDUE MG A 202
07
AC7
SOFTWARE
DCP B:101 , ASP B:423 , MET B:424 , ASP B:570
BINDING SITE FOR RESIDUE MG B 203
08
AC8
SOFTWARE
DCP C:101 , ASP C:423 , MET C:424 , ASP C:570
BINDING SITE FOR RESIDUE MG C 205
09
AC9
SOFTWARE
DCP C:101 , SER C:568 , ASP C:570 , GLU C:571 , DOC I:12
BINDING SITE FOR RESIDUE MG C 206
10
BC1
SOFTWARE
DCP D:101 , MG D:208 , ASP D:423 , MET D:424 , ASP D:570
BINDING SITE FOR RESIDUE MG D 207
11
BC2
SOFTWARE
DCP D:101 , MG D:207 , ASP D:423 , ASP D:570 , GLU D:571 , DOC K:12
BINDING SITE FOR RESIDUE MG D 208
12
BC3
SOFTWARE
THR A:447 , SER A:448 , GLU A:507 , TYR A:541 , DA F:3
BINDING SITE FOR RESIDUE MG A 209
13
BC4
SOFTWARE
THR D:447 , SER D:448 , GLU D:507 , TYR D:541 , DA L:3
BINDING SITE FOR RESIDUE MG D 210
14
BC5
SOFTWARE
THR A:647 , LEU A:649 , VAL A:652 , DA E:11
BINDING SITE FOR RESIDUE MG A 211
15
BC6
SOFTWARE
THR B:647 , ASN B:648 , LEU B:649 , VAL B:652 , DA G:11
BINDING SITE FOR RESIDUE MG B 212
16
BC7
SOFTWARE
THR C:647 , LEU C:649 , VAL C:652 , DA I:11
BINDING SITE FOR RESIDUE MG C 213
17
BC8
SOFTWARE
THR D:647 , LEU D:649 , VAL D:652 , DA K:11 , HOH K:75
BINDING SITE FOR RESIDUE MG D 214
[
close Site info
]
SAPs(SNPs)/Variants
(5, 20)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_021251 (N373S, chain A/B/C/D, )
2: VAR_029194 (M656V, chain A/B/C/D, )
3: VAR_029195 (L660W, chain A/B/C/D, )
4: VAR_029196 (D700N, chain A/B/C/D, )
5: VAR_029197 (R704Q, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021251
N
373
S
REV1_HUMAN
Polymorphism
3087399
A/B/C/D
N
373
S
2
UniProt
VAR_029194
M
656
V
REV1_HUMAN
Polymorphism
3087394
A/B/C/D
M
656
V
3
UniProt
VAR_029195
L
660
W
REV1_HUMAN
Polymorphism
3087398
A/B/C/D
L
660
W
4
UniProt
VAR_029196
D
700
N
REV1_HUMAN
Polymorphism
28382941
A/B/C/D
D
700
N
5
UniProt
VAR_029197
R
704
Q
REV1_HUMAN
Polymorphism
28382942
A/B/C/D
R
704
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:419-653,B:419-653,C:419-653,D:41...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
REV1_HUMAN
419-653
4
A:419-653
B:419-653
C:419-653
D:419-653
[
close PROSITE info
]
Exons
(11, 44)
Info
All Exons
Exon 1.7a (A:344-391 (gaps) | B:344-392 | C:3...)
Exon 1.9b (A:416-441 | B:416-441 | C:416-441 ...)
Exon 1.10 (A:441-477 | B:441-473 | C:441-472 ...)
Exon 1.12a (A:499-516 | B:496-516 | C:500-516 ...)
Exon 1.14b (A:516-559 | B:516-559 | C:516-559 ...)
Exon 1.15 (A:559-611 | B:559-611 | C:559-611 ...)
Exon 1.16b (A:611-651 | B:611-651 | C:611-651 ...)
Exon 1.17b (A:651-724 | B:651-724 | C:651-724 ...)
Exon 1.18a (A:725-782 | B:725-782 | C:725-782 ...)
Exon 1.19b (A:782-816 | B:782-816 | C:782-816 ...)
Exon 1.20b (A:817-828 | B:817-828 | C:817-827 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.6/1.7a
02: Boundary 1.7a/1.9b
03: Boundary 1.9b/1.10
04: Boundary 1.10/1.12a
05: Boundary 1.12a/1.14b
06: Boundary 1.14b/1.15
07: Boundary 1.15/1.16b
08: Boundary 1.16b/1.17b
09: Boundary 1.17b/1.18a
10: Boundary 1.18a/1.19b
11: Boundary 1.19b/1.20b
12: Boundary 1.20b/1.20h
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
1.1a
ENST00000258428
1a
ENSE00001515354
chr2:
100106497-100106279
219
REV1_HUMAN
-
0
0
-
-
1.2
ENST00000258428
2
ENSE00000921861
chr2:
100081447-100081384
64
REV1_HUMAN
1-18
18
0
-
-
1.3b
ENST00000258428
3b
ENSE00000921860
chr2:
100079084-100078958
127
REV1_HUMAN
19-61
43
0
-
-
1.5
ENST00000258428
5
ENSE00001637671
chr2:
100065966-100065798
169
REV1_HUMAN
61-117
57
0
-
-
1.6
ENST00000258428
6
ENSE00001757863
chr2:
100058931-100058779
153
REV1_HUMAN
117-168
52
0
-
-
1.7a
ENST00000258428
7a
ENSE00001698319
chr2:
100055772-100055063
710
REV1_HUMAN
168-405
238
4
A:344-391 (gaps)
B:344-392
C:344-385 (gaps)
D:346-389
48
49
42
44
1.9b
ENST00000258428
9b
ENSE00001623485
chr2:
100052403-100052296
108
REV1_HUMAN
405-441
37
4
A:416-441
B:416-441
C:416-441
D:416-441
26
26
26
26
1.10
ENST00000258428
10
ENSE00001751683
chr2:
100050910-100050794
117
REV1_HUMAN
441-480
40
4
A:441-477
B:441-473
C:441-472
D:441-472
37
33
32
32
1.12a
ENST00000258428
12a
ENSE00000921854
chr2:
100046410-100046302
109
REV1_HUMAN
480-516
37
4
A:499-516
B:496-516
C:500-516
D:496-516
18
21
17
21
1.14b
ENST00000258428
14b
ENSE00001685794
chr2:
100040742-100040614
129
REV1_HUMAN
516-559
44
4
A:516-559
B:516-559
C:516-559
D:516-559
44
44
44
44
1.15
ENST00000258428
15
ENSE00001749185
chr2:
100038115-100037961
155
REV1_HUMAN
559-611
53
4
A:559-611
B:559-611
C:559-611
D:559-611
53
53
53
53
1.16b
ENST00000258428
16b
ENSE00001690779
chr2:
100035409-100035290
120
REV1_HUMAN
611-651
41
4
A:611-651
B:611-651
C:611-651
D:611-651
41
41
41
41
1.17b
ENST00000258428
17b
ENSE00001626429
chr2:
100029413-100029193
221
REV1_HUMAN
651-724
74
4
A:651-724
B:651-724
C:651-724
D:651-724
74
74
74
74
1.18a
ENST00000258428
18a
ENSE00001733763
chr2:
100027329-100027157
173
REV1_HUMAN
725-782
58
4
A:725-782
B:725-782
C:725-782
D:725-782
58
58
58
58
1.19b
ENST00000258428
19b
ENSE00001627924
chr2:
100024593-100024491
103
REV1_HUMAN
782-816
35
4
A:782-816
B:782-816
C:782-816
D:782-816
35
35
35
35
1.20b
ENST00000258428
20b
ENSE00001802837
chr2:
100022952-100022787
166
REV1_HUMAN
817-872
56
4
A:817-828
B:817-828
C:817-827
D:817-827
12
12
11
11
1.20h
ENST00000258428
20h
ENSE00001790412
chr2:
100022568-100022372
197
REV1_HUMAN
872-937
66
0
-
-
1.21
ENST00000258428
21
ENSE00001641934
chr2:
100021140-100020907
234
REV1_HUMAN
938-1015
78
0
-
-
1.22
ENST00000258428
22
ENSE00001774065
chr2:
100020278-100020158
121
REV1_HUMAN
1016-1056
41
0
-
-
1.23d
ENST00000258428
23d
ENSE00001793684
chr2:
100019569-100019352
218
REV1_HUMAN
1056-1128
73
0
-
-
1.24a
ENST00000258428
24a
ENSE00000921842
chr2:
100019263-100019107
157
REV1_HUMAN
1129-1181
53
0
-
-
1.24e
ENST00000258428
24e
ENSE00000921841
chr2:
100018809-100018707
103
REV1_HUMAN
1181-1215
35
0
-
-
1.25b
ENST00000258428
25b
ENSE00000921840
chr2:
100017815-100016938
878
REV1_HUMAN
1215-1251
37
0
-
-
[
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SCOP Domains
(0, 0)
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CATH Domains
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all CATH domains
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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 (323 KB)
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