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3L2P
Asym. Unit
Info
Asym.Unit (222 KB)
Biol.Unit 1 (214 KB)
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(1)
Title
:
HUMAN DNA LIGASE III RECOGNIZES DNA ENDS BY DYNAMIC SWITCHING BETWEEN TWO DNA BOUND STATES
Authors
:
E. A. Cotner-Gohara, I. K. Kim, M. Hammel, J. A. Tainer, A. Tomkinson, T. Ellenberger
Date
:
15 Dec 09 (Deposition) - 14 Jul 10 (Release) - 11 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Dna Ligase, Dna Repair, Atp-Binding, Cell Cycle, Cell Division, Dna Damage, Dna Recombination, Dna Replication, Ligase, Magnesium, Metal-Binding, Nucleotide-Binding, Nucleus, Phosphoprotein, Zinc- Finger, Ligase-Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Cotner-Gohara, I. K. Kim, M. Hammel, J. A. Tainer, A. E. Tomkinson, T. Ellenberger
Human Dna Ligase Iii Recognizes Dna Ends By Dynamic Switching Between Two Dna-Bound States.
Biochemistry V. 49 6165 2010
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
1
Ligand/Ion
ADENOSINE MONOPHOSPHATE
[
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:419 , ILE A:420 , LYS A:421 , TYR A:422 , ARG A:426 , PHE A:508 , LYS A:573 , TRP A:586 , LYS A:588 , LYS A:590 , DG C:12
BINDING SITE FOR RESIDUE AMP A 901
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036513 (D630N, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_036513
D
717
N
DNLI3_HUMAN
Unclassified
---
A
D
630
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: DNA_LIGASE_A1 (A:419-427)
2: DNA_LIGASE_A3 (A:496-630)
3: DNA_LIGASE_A2 (A:568-590)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_LIGASE_A1
PS00697
ATP-dependent DNA ligase AMP-binding site.
DNLI3_HUMAN
506-514
1
A:419-427
2
DNA_LIGASE_A3
PS50160
ATP-dependent DNA ligase family profile.
DNLI3_HUMAN
583-717
1
A:496-630
3
DNA_LIGASE_A2
PS00333
ATP-dependent DNA ligase signature 2.
DNLI3_HUMAN
655-677
1
A:568-590
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Exons
(14, 14)
Info
All Exons
Exon 1.4a (A:168-206)
Exon 1.5 (A:214-260)
Exon 1.6 (A:261-316)
Exon 1.7 (A:316-342)
Exon 1.8 (A:342-398 (gaps))
Exon 1.9 (A:399-450)
Exon 1.10 (A:451-494)
Exon 1.11 (A:495-521)
Exon 1.12b (A:521-550)
Exon 1.12c (A:551-576)
Exon 1.13a (A:577-618 (gaps))
Exon 1.13c (A:618-665)
Exon 1.15 (A:692-739)
Exon 1.16 (A:740-746)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3/1.4a
02: Boundary 1.4a/1.5
03: Boundary 1.5/1.6
04: Boundary 1.6/1.7
05: Boundary 1.7/1.8
06: Boundary 1.8/1.9
07: Boundary 1.9/1.10
08: Boundary 1.10/1.11
09: Boundary 1.11/1.12b
10: Boundary 1.12b/1.12c
11: Boundary 1.12c/1.13a
12: Boundary 1.13a/1.13c
13: Boundary 1.13c/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16
16: Boundary 1.16/1.17a
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
ENST00000378526
1a
ENSE00001429066
chr17:
33307542-33307641
100
DNLI3_HUMAN
-
0
0
-
-
1.2
ENST00000378526
2
ENSE00002172590
chr17:
33310021-33310571
551
DNLI3_HUMAN
1-183
183
0
-
-
1.3
ENST00000378526
3
ENSE00000903608
chr17:
33313007-33313150
144
DNLI3_HUMAN
183-231
49
0
-
-
1.4a
ENST00000378526
4a
ENSE00001106043
chr17:
33316485-33316682
198
DNLI3_HUMAN
231-297
67
1
A:168-206
39
1.5
ENST00000378526
5
ENSE00001160722
chr17:
33317982-33318133
152
DNLI3_HUMAN
297-347
51
1
A:214-260
47
1.6
ENST00000378526
6
ENSE00001106042
chr17:
33318690-33318856
167
DNLI3_HUMAN
348-403
56
1
A:261-316
56
1.7
ENST00000378526
7
ENSE00001106051
chr17:
33318977-33319054
78
DNLI3_HUMAN
403-429
27
1
A:316-342
27
1.8
ENST00000378526
8
ENSE00001106059
chr17:
33319543-33319711
169
DNLI3_HUMAN
429-485
57
1
A:342-398 (gaps)
57
1.9
ENST00000378526
9
ENSE00001106065
chr17:
33321295-33321450
156
DNLI3_HUMAN
486-537
52
1
A:399-450
52
1.10
ENST00000378526
10
ENSE00000713847
chr17:
33323083-33323214
132
DNLI3_HUMAN
538-581
44
1
A:451-494
44
1.11
ENST00000378526
11
ENSE00000887588
chr17:
33323593-33323672
80
DNLI3_HUMAN
582-608
27
1
A:495-521
27
1.12b
ENST00000378526
12b
ENSE00000343039
chr17:
33324757-33324844
88
DNLI3_HUMAN
608-637
30
1
A:521-550
30
1.12c
ENST00000378526
12c
ENSE00000343040
chr17:
33325238-33325315
78
DNLI3_HUMAN
638-663
26
1
A:551-576
26
1.13a
ENST00000378526
13a
ENSE00000713843
chr17:
33325623-33325746
124
DNLI3_HUMAN
664-705
42
1
A:577-618 (gaps)
42
1.13c
ENST00000378526
13c
ENSE00000887592
chr17:
33326326-33326468
143
DNLI3_HUMAN
705-752
48
1
A:618-665
48
1.14
ENST00000378526
14
ENSE00000887593
chr17:
33326801-33326875
75
DNLI3_HUMAN
753-777
25
0
-
-
1.15
ENST00000378526
15
ENSE00000887594
chr17:
33328276-33328422
147
DNLI3_HUMAN
778-826
49
1
A:692-739
48
1.16
ENST00000378526
16
ENSE00000343045
chr17:
33328928-33329123
196
DNLI3_HUMAN
827-892
66
1
A:740-746
7
1.17a
ENST00000378526
17a
ENSE00000713836
chr17:
33329687-33329808
122
DNLI3_HUMAN
892-932
41
0
-
-
1.17d
ENST00000378526
17d
ENSE00001160861
chr17:
33331292-33332083
792
DNLI3_HUMAN
933-1009
77
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_DNA_ligase_A_M_3l2pA01 (A:396-590)
2a: PFAM_DNA_ligase_A_C_3l2pA02 (A:617-727)
3a: PFAM_DNA_ligase_A_N_3l2pA03 (A:174-348)
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Clans
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(
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Families
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(
)
Organisms
(
)
(
)
Clan
:
DNA_ligase
(17)
Family
:
DNA_ligase_A_M
(7)
Homo sapiens (Human)
(2)
1a
DNA_ligase_A_M-3l2pA01
A:396-590
Clan
:
no clan defined [family: DNA_ligase_A_C]
(2)
Family
:
DNA_ligase_A_C
(2)
Homo sapiens (Human)
(2)
2a
DNA_ligase_A_C-3l2pA02
A:617-727
Clan
:
no clan defined [family: DNA_ligase_A_N]
(2)
Family
:
DNA_ligase_A_N
(2)
Homo sapiens (Human)
(2)
3a
DNA_ligase_A_N-3l2pA03
A:174-348
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