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SMTL ID : 7l34.1
Human DNA Ligase 1 - R641L nicked DNA complex
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
monomer
Ligands
1 x
DG
-
DT
-
DC
-
DG
-
DG
-
DA
-
DC
:
DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
(Non-covalent)
DG-DT-DC-DG-DG-DA-DC.1:
28 residues within 4Å:
Chain A:
S.44
,
A.45
,
R.46
,
R.290
,
K.309
,
R.330
,
K.485
,
K.487
,
Y.490
,
K.511
,
T.539
,
G.540
,
F.541
,
S.542
,
D.543
,
E.544
,
F.613
,
R.615
Chain B:
C.11
Chain C:
G.1
,
T.2
,
C.3
,
C.4
,
G.5
,
A.6
,
C.7
,
G.8
Ligands:
AMP.2
43
PLIP interactions
:
43 interactions with chain A
Hydrophobic interactions:
A:R.512
Hydrogen bonds:
A:L.193
,
A:G.194
,
A:L.195
,
A:A.196
,
A:A.196
,
A:Q.198
,
A:S.199
,
A:S.199
,
A:Q.377
,
A:T.380
,
A:R.509
,
A:K.511
,
A:K.511
,
A:K.536
,
A:S.591
,
A:S.593
,
A:S.593
,
A:Y.596
Water bridges:
A:R.46
,
A:R.190
,
A:R.190
,
A:R.190
,
A:R.190
,
A:L.195
,
A:K.245
,
A:R.479
,
A:R.479
,
A:R.512
,
A:R.512
,
A:G.517
,
A:K.536
,
A:G.538
,
A:T.539
,
A:T.539
,
A:R.612
,
A:F.613
Salt bridges:
A:R.190
,
A:R.192
,
A:R.298
,
A:R.479
,
A:K.536
,
A:K.536
1 x
AMP
:
ADENOSINE MONOPHOSPHATE
(Non-covalent)
AMP.2:
17 residues within 4Å:
Chain A:
A.286
,
E.307
,
Y.308
,
K.309
,
Y.310
,
R.314
,
R.330
,
E.362
,
F.401
,
A.437
,
M.464
,
K.466
,
W.483
,
K.485
,
K.487
Chain B:
C.11
Ligands:
DG-DT-DC-DG-DG-DA-DC.1
11
PLIP interactions
:
11 interactions with chain A
Hydrogen bonds:
A:E.307
,
A:K.309
,
A:Y.310
,
A:R.314
,
A:R.330
,
A:K.466
Water bridges:
A:R.314
Salt bridges:
A:K.309
,
A:K.485
,
A:K.487
pi-Stacking:
A:F.401
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Jurkiw, T.J. et al., LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency. Nucleic Acids Res. (2021)
Release Date
2021-01-13
Peptides
DNA ligase 1:
A
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
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DNA ligase 1
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