1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
DeRose, E.F.
Kirby, T.W.
Mueller, G.A.
Bebenek, K.
Garcia-Diaz, M.
Blanco, L.
Kunkel, T.A.
London, R.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Biochemistry
BICHAW
0033
0006-2960
42
9564
9574
10.1021/bi034298s
12911298
Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda
2003
10.2210/pdb1nzp/pdb
pdb_00001nzp
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
9715.243
DNA polymerase lambda
2.7.7.7
POLYMERASE LAMBDA LYASE DOMAIN(RESIDUES 242 - 327)
1
man
polymer
Pol Lambda, DNA polymerase Lambda, DNA polymerase beta-2, Pol beta2
no
no
MAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESG
HLRKLDH
MAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESG
HLRKLDH
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
Escherichia
sample
POLL
9606
Homo sapiens
562
Escherichia coli
BLR (DE3)
PLASMID
pET30a(+)
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2003-08-05
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
RCSB
Y
RCSB
2003-02-19
REL
REL
Chemical shift assigments were made from 3D HNCACB,
CBCA(CO)NH, HNCO, H(CCO)NH, and (H)C(CO)NH experiments.
Aromatic resonances were assigned using 2D (HB)CB(CGCD)HD
and (HB)CB(CGCDCE)HE experiments.
structures with the lowest energy
20
8
3D_13C-separated_NOESY
3D_15N-separated_NOESY
5mM Tris, 100mM NaCl, 5mM NaN3
7
ambient
298
K
The structure was computed using default ARIA parameters.
281 manually assigned NOE distance restraints were used
in addition to the NOE restraints automatically assigned
by ARIA. ARIA assigned 790 unambiguous and 191 ambiguous
NOE restraints.
simulated annealing
torsion angle dynamics follow by cartesian dynamics
1
minimized average structure
2mM pol lambda 8 kDa domain U-15N,13C; 5mM Tris-d11; 100mM NaCl; 1mM DTT; 5mM NaN3
90% H2O/10% D2O
Varian, Inc.
collection
VNMR
6.1C
F. Delaglio
processing
NMRPipe
2.1
B.A. Johnson
data analysis
NMRView
5.0.4
A.T., Brunger et al.
structure solution
CNS
1.0
M. Nilges
structure solution
ARIA
1.1
M. Nilges
refinement
ARIA
1.1
600
Varian
INOVA
n
1
241
A
ALA
242
n
2
ALA
242
A
GLN
243
n
3
GLN
243
A
PRO
244
n
4
PRO
244
A
SER
245
n
5
SER
245
A
SER
246
n
6
SER
246
A
GLN
247
n
7
GLN
247
A
LYS
248
n
8
LYS
248
A
ALA
249
n
9
ALA
249
A
THR
250
n
10
THR
250
A
ASN
251
n
11
ASN
251
A
HIS
252
n
12
HIS
252
A
ASN
253
n
13
ASN
253
A
LEU
254
n
14
LEU
254
A
HIS
255
n
15
HIS
255
A
ILE
256
n
16
ILE
256
A
THR
257
n
17
THR
257
A
GLU
258
n
18
GLU
258
A
LYS
259
n
19
LYS
259
A
LEU
260
n
20
LEU
260
A
GLU
261
n
21
GLU
261
A
VAL
262
n
22
VAL
262
A
LEU
263
n
23
LEU
263
A
ALA
264
n
24
ALA
264
A
LYS
265
n
25
LYS
265
A
ALA
266
n
26
ALA
266
A
TYR
267
n
27
TYR
267
A
SER
268
n
28
SER
268
A
VAL
269
n
29
VAL
269
A
GLN
270
n
30
GLN
270
A
GLY
271
n
31
GLY
271
A
ASP
272
n
32
ASP
272
A
LYS
273
n
33
LYS
273
A
TRP
274
n
34
TRP
274
A
ARG
275
n
35
ARG
275
A
ALA
276
n
36
ALA
276
A
LEU
277
n
37
LEU
277
A
GLY
278
n
38
GLY
278
A
TYR
279
n
39
TYR
279
A
ALA
280
n
40
ALA
280
A
LYS
281
n
41
LYS
281
A
ALA
282
n
42
ALA
282
A
ILE
283
n
43
ILE
283
A
ASN
284
n
44
ASN
284
A
ALA
285
n
45
ALA
285
A
LEU
286
n
46
LEU
286
A
LYS
287
n
47
LYS
287
A
SER
288
n
48
SER
288
A
PHE
289
n
49
PHE
289
A
HIS
290
n
50
HIS
290
A
LYS
291
n
51
LYS
291
A
PRO
292
n
52
PRO
292
A
VAL
293
n
53
VAL
293
A
THR
294
n
54
THR
294
A
SER
295
n
55
SER
295
A
TYR
296
n
56
TYR
296
A
GLN
297
n
57
GLN
297
A
GLU
298
n
58
GLU
298
A
ALA
299
n
59
ALA
299
A
CYS
300
n
60
CYS
300
A
SER
301
n
61
SER
301
A
ILE
302
n
62
ILE
302
A
PRO
303
n
63
PRO
303
A
GLY
304
n
64
GLY
304
A
ILE
305
n
65
ILE
305
A
GLY
306
n
66
GLY
306
A
LYS
307
n
67
LYS
307
A
ARG
308
n
68
ARG
308
A
MET
309
n
69
MET
309
A
ALA
310
n
70
ALA
310
A
GLU
311
n
71
GLU
311
A
LYS
312
n
72
LYS
312
A
ILE
313
n
73
ILE
313
A
ILE
314
n
74
ILE
314
A
GLU
315
n
75
GLU
315
A
ILE
316
n
76
ILE
316
A
LEU
317
n
77
LEU
317
A
GLU
318
n
78
GLU
318
A
SER
319
n
79
SER
319
A
GLY
320
n
80
GLY
320
A
HIS
321
n
81
HIS
321
A
LEU
322
n
82
LEU
322
A
ARG
323
n
83
ARG
323
A
LYS
324
n
84
LYS
324
A
LEU
325
n
85
LEU
325
A
ASP
326
n
86
ASP
326
A
HIS
327
n
87
HIS
327
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
MET
241
A
MET
1
1
Y
2
A
MET
241
A
MET
1
1
Y
3
A
MET
241
A
MET
1
1
Y
4
A
MET
241
A
MET
1
1
Y
5
A
MET
241
A
MET
1
1
Y
6
A
MET
241
A
MET
1
1
Y
7
A
MET
241
A
MET
1
1
Y
8
A
MET
241
A
MET
1
1
Y
1
A
PRO
244
-78.91
-119.91
1
A
SER
245
58.61
89.10
1
A
LYS
248
-129.58
-162.26
1
A
ASN
251
-58.70
174.28
1
A
ASN
253
-99.70
-81.89
1
A
LEU
254
58.56
-2.32
1
A
PRO
292
-66.17
-173.87
1
A
THR
294
-138.75
-40.26
1
A
HIS
321
-146.90
-74.62
1
A
LEU
322
-129.37
-72.07
2
A
SER
246
-168.64
10.82
2
A
ASN
253
-157.92
49.32
2
A
ASP
272
-66.36
87.18
2
A
THR
294
-136.39
-32.75
2
A
GLU
318
71.16
-34.14
2
A
SER
319
58.24
109.25
2
A
HIS
321
-144.98
11.83
3
A
GLN
243
56.20
84.76
3
A
PRO
244
-80.00
47.36
3
A
LYS
248
55.02
77.42
3
A
HIS
255
-65.99
2.35
3
A
THR
294
-131.13
-40.65
3
A
GLU
318
-141.45
-106.15
3
A
SER
319
47.31
94.34
3
A
LEU
322
-59.00
84.22
3
A
ARG
323
-55.79
101.52
4
A
PRO
244
-66.24
-175.95
4
A
SER
245
-168.43
-31.48
4
A
SER
246
60.55
-86.74
4
A
GLN
247
58.80
-162.79
4
A
HIS
252
-131.36
-56.16
4
A
ASN
253
-138.22
-68.03
4
A
LEU
254
39.36
37.25
4
A
ASP
272
-157.22
84.38
4
A
GLU
318
-42.09
-82.90
5
A
GLN
247
62.91
-83.80
5
A
SER
288
-153.35
21.11
5
A
HIS
290
-107.63
-66.55
5
A
PRO
292
-48.87
155.25
5
A
THR
294
-133.13
-43.55
5
A
GLU
318
-68.92
-90.09
5
A
SER
319
50.32
-96.62
6
A
SER
246
-70.95
-81.89
6
A
GLN
247
-167.75
-12.86
6
A
PRO
292
-68.96
-173.77
6
A
GLU
318
59.65
7.57
7
A
SER
246
-130.11
-77.12
7
A
LYS
248
-103.60
71.19
7
A
THR
250
-47.05
106.61
7
A
ASN
253
-150.04
19.72
7
A
HIS
255
-91.57
-65.44
7
A
ASP
272
-68.44
92.30
7
A
LYS
291
136.46
-51.34
7
A
PRO
292
-47.54
97.78
7
A
PRO
303
-65.63
5.98
7
A
GLU
318
-87.02
-76.87
7
A
SER
319
57.15
17.33
7
A
LEU
322
-130.28
-63.43
8
A
PRO
244
-79.02
-119.84
8
A
SER
245
58.57
89.11
8
A
LYS
248
-129.52
-162.18
8
A
ASN
251
-58.79
174.28
8
A
ASN
253
-99.68
-81.92
8
A
LEU
254
58.55
-2.24
8
A
PRO
292
-66.15
-173.90
8
A
THR
294
-138.75
-40.42
8
A
HIS
321
-146.95
-74.63
8
A
LEU
322
-129.34
-72.09
minimized average
Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda
1
N
N
A
LEU
254
A
LEU
14
HELX_P
A
GLY
271
A
GLY
31
1
1
18
A
ASP
272
A
ASP
32
HELX_P
A
LYS
287
A
LYS
47
1
2
16
A
SER
295
A
SER
55
HELX_P
A
SER
301
A
SER
61
1
3
7
A
GLY
306
A
GLY
66
HELX_P
A
GLU
318
A
GLU
78
1
4
13
DNA BINDING PROTEIN/TRANSFERASE
DNA POLYMERASE LAMBDA, POL LAMBDA, LYASE DOMAIN, 8 kDa DOMAIN, POL BETA-LIKE, DNA BINDING PROTEIN-TRANSFERASE COMPLEX
DPOL_HUMAN
UNP
1
242
Q9UGP5
AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGH
LRKLDH
242
327
1NZP
242
327
Q9UGP5
A
1
2
87
1
cloning artifact
MET
241
1NZP
A
Q9UGP5
UNP
1