1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Ikegami, T.
Kuraoka, I.
Saijo, M.
Kodo, N.
Kyogoku, Y.
Morikawa, K.
Tanaka, K.
Shirakawa, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
Zn 2
65.409
ZINC ION
non-polymer
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
5
701
706
10.1038/1400
9699634
Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA.
1998
10.2210/pdb1xpa/pdb
pdb_00001xpa
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
14728.981
XPA
MF122, RESIDUES 98-219
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
no
no
MEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGD
MKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKF
MEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGD
MKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKF
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
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
Escherichia coli
sample
9606
Homo sapiens
HUMAN XPA CDNA
511693
Escherichia coli BL21
BL21
PET16B
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1999-07-22
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-03-02
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1998-07-06
REL
REL
ZN
ZINC ION
THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED XPA. THIS MODEL IS THE CLOSEST STRUCTURE TO THE MEAN.
THE LOWEST ENERGY AND NO VIOLATION GREATER THAN 0.3A OR 5DEG
140
1
3D-
4D-MULTI-DIMENSIONAL EXPERIMENTS
150mM KCL
7.3
1
ATMOSPHERE
303
K
distance geometry
50MM D-TRIS HCL
structure solution
X-PLOR
3.1
refinement
X-PLOR
3.1
500
Bruker
DMX500
800
Bruker
DRX500
800
Bruker
DRX800
ZN
220
2
ZN
ZN
220
A
MET
98
n
1
MET
98
A
GLU
99
n
2
GLU
99
A
PHE
100
n
3
PHE
100
A
ASP
101
n
4
ASP
101
A
TYR
102
n
5
TYR
102
A
VAL
103
n
6
VAL
103
A
ILE
104
n
7
ILE
104
A
CYS
105
n
8
CYS
105
A
GLU
106
n
9
GLU
106
A
GLU
107
n
10
GLU
107
A
CYS
108
n
11
CYS
108
A
GLY
109
n
12
GLY
109
A
LYS
110
n
13
LYS
110
A
GLU
111
n
14
GLU
111
A
PHE
112
n
15
PHE
112
A
MET
113
n
16
MET
113
A
ASP
114
n
17
ASP
114
A
SER
115
n
18
SER
115
A
TYR
116
n
19
TYR
116
A
LEU
117
n
20
LEU
117
A
MET
118
n
21
MET
118
A
ASN
119
n
22
ASN
119
A
HIS
120
n
23
HIS
120
A
PHE
121
n
24
PHE
121
A
ASP
122
n
25
ASP
122
A
LEU
123
n
26
LEU
123
A
PRO
124
n
27
PRO
124
A
THR
125
n
28
THR
125
A
CYS
126
n
29
CYS
126
A
ASP
127
n
30
ASP
127
A
ASN
128
n
31
ASN
128
A
CYS
129
n
32
CYS
129
A
ARG
130
n
33
ARG
130
A
ASP
131
n
34
ASP
131
A
ALA
132
n
35
ALA
132
A
ASP
133
n
36
ASP
133
A
ASP
134
n
37
ASP
134
A
LYS
135
n
38
LYS
135
A
HIS
136
n
39
HIS
136
A
LYS
137
n
40
LYS
137
A
LEU
138
n
41
LEU
138
A
ILE
139
n
42
ILE
139
A
THR
140
n
43
THR
140
A
LYS
141
n
44
LYS
141
A
THR
142
n
45
THR
142
A
GLU
143
n
46
GLU
143
A
ALA
144
n
47
ALA
144
A
LYS
145
n
48
LYS
145
A
GLN
146
n
49
GLN
146
A
GLU
147
n
50
GLU
147
A
TYR
148
n
51
TYR
148
A
LEU
149
n
52
LEU
149
A
LEU
150
n
53
LEU
150
A
LYS
151
n
54
LYS
151
A
ASP
152
n
55
ASP
152
A
CYS
153
n
56
CYS
153
A
ASP
154
n
57
ASP
154
A
LEU
155
n
58
LEU
155
A
GLU
156
n
59
GLU
156
A
LYS
157
n
60
LYS
157
A
ARG
158
n
61
ARG
158
A
GLU
159
n
62
GLU
159
A
PRO
160
n
63
PRO
160
A
PRO
161
n
64
PRO
161
A
LEU
162
n
65
LEU
162
A
LYS
163
n
66
LYS
163
A
PHE
164
n
67
PHE
164
A
ILE
165
n
68
ILE
165
A
VAL
166
n
69
VAL
166
A
LYS
167
n
70
LYS
167
A
LYS
168
n
71
LYS
168
A
ASN
169
n
72
ASN
169
A
PRO
170
n
73
PRO
170
A
HIS
171
n
74
HIS
171
A
HIS
172
n
75
HIS
172
A
SER
173
n
76
SER
173
A
GLN
174
n
77
GLN
174
A
TRP
175
n
78
TRP
175
A
GLY
176
n
79
GLY
176
A
ASP
177
n
80
ASP
177
A
MET
178
n
81
MET
178
A
LYS
179
n
82
LYS
179
A
LEU
180
n
83
LEU
180
A
TYR
181
n
84
TYR
181
A
LEU
182
n
85
LEU
182
A
LYS
183
n
86
LYS
183
A
LEU
184
n
87
LEU
184
A
GLN
185
n
88
GLN
185
A
ILE
186
n
89
ILE
186
A
VAL
187
n
90
VAL
187
A
LYS
188
n
91
LYS
188
A
ARG
189
n
92
ARG
189
A
SER
190
n
93
SER
190
A
LEU
191
n
94
LEU
191
A
GLU
192
n
95
GLU
192
A
VAL
193
n
96
VAL
193
A
TRP
194
n
97
TRP
194
A
GLY
195
n
98
GLY
195
A
SER
196
n
99
SER
196
A
GLN
197
n
100
GLN
197
A
GLU
198
n
101
GLU
198
A
ALA
199
n
102
ALA
199
A
LEU
200
n
103
LEU
200
A
GLU
201
n
104
GLU
201
A
GLU
202
n
105
GLU
202
A
ALA
203
n
106
ALA
203
A
LYS
204
n
107
LYS
204
A
GLU
205
n
108
GLU
205
A
VAL
206
n
109
VAL
206
A
ARG
207
n
110
ARG
207
A
GLN
208
n
111
GLN
208
A
GLU
209
n
112
GLU
209
A
ASN
210
n
113
ASN
210
A
n
114
211
A
n
115
212
A
n
116
213
A
n
117
214
A
n
118
215
A
n
119
216
A
n
120
217
A
n
121
218
A
n
122
219
A
author_defined_assembly
1
monomeric
A
CYS
105
A
SG
CYS
8
1_555
A
ZN
220
B
ZN
ZN
1_555
A
CYS
108
A
SG
CYS
11
1_555
106.3
A
CYS
105
A
SG
CYS
8
1_555
A
ZN
220
B
ZN
ZN
1_555
A
CYS
126
A
SG
CYS
29
1_555
112.1
A
CYS
108
A
SG
CYS
11
1_555
A
ZN
220
B
ZN
ZN
1_555
A
CYS
126
A
SG
CYS
29
1_555
109.9
A
CYS
105
A
SG
CYS
8
1_555
A
ZN
220
B
ZN
ZN
1_555
A
CYS
129
A
SG
CYS
32
1_555
106.8
A
CYS
108
A
SG
CYS
11
1_555
A
ZN
220
B
ZN
ZN
1_555
A
CYS
129
A
SG
CYS
32
1_555
112.2
A
CYS
126
A
SG
CYS
29
1_555
A
ZN
220
B
ZN
ZN
1_555
A
CYS
129
A
SG
CYS
32
1_555
109.4
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
A
O
VAL
103
A
O
VAL
6
A
N
PHE
112
A
N
PHE
15
A
O
ILE
139
A
O
ILE
42
A
N
TYR
181
A
N
TYR
84
A
O
LEU
180
A
O
LEU
83
A
N
ILE
165
A
N
ILE
68
1
A
ARG
211
A
ARG
114
1
Y
1
A
GLU
212
A
GLU
115
1
Y
1
A
LYS
213
A
LYS
116
1
Y
1
A
MET
214
A
MET
117
1
Y
1
A
LYS
215
A
LYS
118
1
Y
1
A
GLN
216
A
GLN
119
1
Y
1
A
LYS
217
A
LYS
120
1
Y
1
A
LYS
218
A
LYS
121
1
Y
1
A
PHE
219
A
PHE
122
1
Y
1
A
ARG
130
0.281
SIDE CHAIN
1
A
ARG
158
0.269
SIDE CHAIN
1
A
ARG
189
0.317
SIDE CHAIN
1
A
ARG
207
0.307
SIDE CHAIN
1
A
TYR
102
-152.09
33.45
1
A
GLU
107
-125.52
-50.88
1
A
SER
115
-157.32
-147.12
1
A
ASP
134
-160.23
-56.71
1
A
LYS
135
-46.33
-74.72
1
A
LYS
137
-48.69
93.46
1
A
LEU
138
-41.88
163.89
1
A
LEU
149
43.70
26.25
1
A
LYS
151
-123.23
-140.44
1
A
CYS
153
-127.97
-86.25
1
A
LEU
155
-125.18
-51.30
1
A
GLU
159
39.13
85.21
1
A
LEU
162
22.23
99.96
1
A
LYS
163
-28.73
128.72
1
A
ILE
165
-153.15
-159.22
1
A
LYS
167
-157.72
-144.64
1
A
HIS
171
-92.58
-155.47
1
A
ASP
177
-158.61
55.81
1
A
LEU
182
-46.18
105.90
1
A
SER
196
179.38
-147.95
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
SOLUTION STRUCTURE OF THE DNA-AND RPA-BINDING DOMAIN OF THE HUMAN REPAIR FACTOR XPA, NMR, 1 STRUCTURE
1
Y
N
2
N
N
A
LYS
141
A
LYS
44
HELX_P
A
GLU
147
A
GLU
50
1
H1
7
A
LYS
183
A
LYS
86
HELX_P
A
TRP
194
A
TRP
97
1
H2
12
A
GLN
197
A
GLN
100
HELX_P
A
GLU
209
A
GLU
112
1
H3
13
metalc
2.257
A
CYS
105
A
SG
CYS
8
1_555
A
ZN
220
B
ZN
ZN
1_555
metalc
2.350
A
CYS
108
A
SG
CYS
11
1_555
A
ZN
220
B
ZN
ZN
1_555
metalc
2.436
A
CYS
126
A
SG
CYS
29
1_555
A
ZN
220
B
ZN
ZN
1_555
metalc
2.353
A
CYS
129
A
SG
CYS
32
1_555
A
ZN
220
B
ZN
ZN
1_555
DNA REPAIR
DNA REPAIR, NUCLEOTIDE EXCISION REPAIR, ZINC-FINGER
A
GLU
159
A
GLU
62
1
A
PRO
160
A
PRO
63
0.07
XPA_HUMAN
UNP
1
1
P23025
MAAADGALPEAAALEQPAELPASVRASIERKRQRALMLRQARLAARPYSATAAAATGGMANVKAAPKIIDTGGGFILEEE
EEEEQKIGKVVHQPGPVMEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREP
PLKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRETI
VHQHEYGPEENLEDDMYRKTCTMCGHELTYEKM
98
219
1XPA
98
219
P23025
A
1
1
122
2
3
anti-parallel
anti-parallel
anti-parallel
A
VAL
103
A
VAL
6
A
ILE
104
A
ILE
7
A
GLU
111
A
GLU
14
A
PHE
112
A
PHE
15
A
ILE
139
A
ILE
42
A
THR
140
A
THR
43
A
LEU
180
A
LEU
83
A
TYR
181
A
TYR
84
A
PHE
164
A
PHE
67
A
ILE
165
A
ILE
68
ZN BINDING SITE.
Unknown
4
BINDING SITE FOR RESIDUE ZN A 220
A
ZN
220
Software
4
A
CYS
105
A
CYS
8
4
1_555
A
CYS
108
A
CYS
11
4
1_555
A
CYS
126
A
CYS
29
4
1_555
A
CYS
129
A
CYS
32
4
1_555
A
CYS
105
A
CYS
8
4
1_555
A
CYS
108
A
CYS
11
4
1_555
A
CYS
126
A
CYS
29
4
1_555
A
CYS
129
A
CYS
32
4
1_555
1
P 1