0.027411
0.000000
0.000000
0.000000
0.013613
0.000000
0.000000
0.000000
0.028859
0.00000
0.00000
0.00000
Suzuki, N.
Wakatsuki, S.
Kawasaki, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
36.482
73.457
34.651
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
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Na 1
22.990
SODIUM ION
non-polymer
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
UK
Febs J.
1742-464X
10.1111/febs.13734
27062441
A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.
2016
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2007-12-05
ADSC QUANTUM 270
Si 111
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
BL-17A
Photon Factory
1.0000
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-17A
3243.759
ATPase WRNIP1
UBIQUITIN-BINDING ZINC FINGER DOMAIN (UNP RESIDUES 17-40)
2
man
polymer
65.409
ZINC ION
2
syn
non-polymer
22.990
SODIUM ION
2
syn
non-polymer
18.015
water
16
nat
water
Werner helicase-interacting protein 1
no
no
GSPEFQVQCPVCQQMMPAAHINSHLDRCL
GSPEFQVQCPVCQQMMPAAHINSHLDRCL
A,B
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
human
sample
WRNIP1, WHIP
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)
PLASMID
pGEX4T-1
1
1.79
31.25
VAPOR DIFFUSION, SITTING DROP
7.5
28% PEG 400, 0.1M HEPES, 0.2M calcium chrolide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
293.0
repository
Initial release
Database references
1
0
2012-10-10
1
1
2016-06-01
PDBJ
Y
PDBJ
2011-09-06
REL
REL
ZN
ZINC ION
NA
SODIUM ION
HOH
water
ZN
51
2
ZN
ZN
51
A
NA
52
3
NA
NA
52
A
ZN
51
2
ZN
ZN
51
B
NA
52
3
NA
NA
52
B
HOH
61
4
HOH
HOH
61
A
HOH
64
4
HOH
HOH
62
A
HOH
63
4
HOH
HOH
63
A
HOH
64
4
HOH
HOH
64
A
HOH
65
4
HOH
HOH
65
A
HOH
66
4
HOH
HOH
66
A
HOH
67
4
HOH
HOH
67
A
HOH
68
4
HOH
HOH
68
A
HOH
69
4
HOH
HOH
69
A
HOH
70
4
HOH
HOH
70
A
HOH
71
4
HOH
HOH
71
A
HOH
72
4
HOH
HOH
72
A
HOH
61
4
HOH
HOH
61
B
HOH
62
4
HOH
HOH
62
B
HOH
63
4
HOH
HOH
63
B
HOH
62
4
HOH
HOH
64
B
n
1
12
A
n
2
13
A
n
3
14
A
n
4
15
A
PHE
16
n
5
PHE
16
A
GLN
17
n
6
GLN
17
A
VAL
18
n
7
VAL
18
A
GLN
19
n
8
GLN
19
A
CYS
20
n
9
CYS
20
A
PRO
21
n
10
PRO
21
A
VAL
22
n
11
VAL
22
A
CYS
23
n
12
CYS
23
A
GLN
24
n
13
GLN
24
A
GLN
25
n
14
GLN
25
A
MET
26
n
15
MET
26
A
MET
27
n
16
MET
27
A
PRO
28
n
17
PRO
28
A
ALA
29
n
18
ALA
29
A
ALA
30
n
19
ALA
30
A
HIS
31
n
20
HIS
31
A
ILE
32
n
21
ILE
32
A
ASN
33
n
22
ASN
33
A
SER
34
n
23
SER
34
A
HIS
35
n
24
HIS
35
A
LEU
36
n
25
LEU
36
A
ASP
37
n
26
ASP
37
A
ARG
38
n
27
ARG
38
A
CYS
39
n
28
CYS
39
A
LEU
40
n
29
LEU
40
A
n
1
12
B
n
2
13
B
n
3
14
B
GLU
15
n
4
GLU
15
B
PHE
16
n
5
PHE
16
B
GLN
17
n
6
GLN
17
B
VAL
18
n
7
VAL
18
B
GLN
19
n
8
GLN
19
B
CYS
20
n
9
CYS
20
B
PRO
21
n
10
PRO
21
B
VAL
22
n
11
VAL
22
B
CYS
23
n
12
CYS
23
B
GLN
24
n
13
GLN
24
B
GLN
25
n
14
GLN
25
B
MET
26
n
15
MET
26
B
MET
27
n
16
MET
27
B
PRO
28
n
17
PRO
28
B
ALA
29
n
18
ALA
29
B
ALA
30
n
19
ALA
30
B
HIS
31
n
20
HIS
31
B
ILE
32
n
21
ILE
32
B
ASN
33
n
22
ASN
33
B
SER
34
n
23
SER
34
B
HIS
35
n
24
HIS
35
B
LEU
36
n
25
LEU
36
B
ASP
37
n
26
ASP
37
B
ARG
38
n
27
ARG
38
B
CYS
39
n
28
CYS
39
B
LEU
40
n
29
LEU
40
B
author_and_software_defined_assembly
PISA
2
dimeric
1140
-92
3880
A
HIS
35
A
NE2
HIS
24
1_555
A
ZN
51
C
ZN
ZN
1_555
A
CYS
20
A
SG
CYS
9
1_555
110.2
A
HIS
35
A
NE2
HIS
24
1_555
A
ZN
51
C
ZN
ZN
1_555
A
CYS
23
A
SG
CYS
12
1_555
107.8
A
CYS
20
A
SG
CYS
9
1_555
A
ZN
51
C
ZN
ZN
1_555
A
CYS
23
A
SG
CYS
12
1_555
109.4
A
HIS
35
A
NE2
HIS
24
1_555
A
ZN
51
C
ZN
ZN
1_555
A
HOH
61
G
O
HOH
1_555
108.3
A
CYS
20
A
SG
CYS
9
1_555
A
ZN
51
C
ZN
ZN
1_555
A
HOH
61
G
O
HOH
1_555
108.4
A
CYS
23
A
SG
CYS
12
1_555
A
ZN
51
C
ZN
ZN
1_555
A
HOH
61
G
O
HOH
1_555
112.8
A
HIS
31
A
NE2
HIS
20
1_555
B
ZN
51
E
ZN
ZN
1_555
B
HIS
35
B
NE2
HIS
24
1_555
101.7
A
HIS
31
A
NE2
HIS
20
1_555
B
ZN
51
E
ZN
ZN
1_555
B
CYS
23
B
SG
CYS
12
1_555
110.5
B
HIS
35
B
NE2
HIS
24
1_555
B
ZN
51
E
ZN
ZN
1_555
B
CYS
23
B
SG
CYS
12
1_555
117.5
A
HIS
31
A
NE2
HIS
20
1_555
B
ZN
51
E
ZN
ZN
1_555
B
CYS
20
B
SG
CYS
9
1_555
111.4
B
HIS
35
B
NE2
HIS
24
1_555
B
ZN
51
E
ZN
ZN
1_555
B
CYS
20
B
SG
CYS
9
1_555
100.1
B
CYS
23
B
SG
CYS
12
1_555
B
ZN
51
E
ZN
ZN
1_555
B
CYS
20
B
SG
CYS
9
1_555
114.6
A
MET
26
A
O
MET
15
1_555
B
NA
52
F
NA
NA
1_555
B
ASP
37
B
OD2
ASP
26
1_555
86.1
A
MET
26
A
O
MET
15
1_555
B
NA
52
F
NA
NA
1_555
B
ASP
37
B
OD1
ASP
26
1_555
109.1
B
ASP
37
B
OD2
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
B
ASP
37
B
OD1
ASP
26
1_555
48.4
A
MET
26
A
O
MET
15
1_555
B
NA
52
F
NA
NA
1_555
B
HOH
62
H
O
HOH
1_555
93.5
B
ASP
37
B
OD2
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
B
HOH
62
H
O
HOH
1_555
105.9
B
ASP
37
B
OD1
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
B
HOH
62
H
O
HOH
1_555
62.9
A
MET
26
A
O
MET
15
1_555
B
NA
52
F
NA
NA
1_555
B
HOH
64
H
O
HOH
1_555
117.2
B
ASP
37
B
OD2
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
B
HOH
64
H
O
HOH
1_555
76.0
B
ASP
37
B
OD1
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
B
HOH
64
H
O
HOH
1_555
102.1
B
HOH
62
H
O
HOH
1_555
B
NA
52
F
NA
NA
1_555
B
HOH
64
H
O
HOH
1_555
149.3
A
MET
26
A
O
MET
15
1_555
B
NA
52
F
NA
NA
1_555
A
HOH
69
G
O
HOH
1_555
84.2
B
ASP
37
B
OD2
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
A
HOH
69
G
O
HOH
1_555
152.0
B
ASP
37
B
OD1
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
A
HOH
69
G
O
HOH
1_555
158.8
B
HOH
62
H
O
HOH
1_555
B
NA
52
F
NA
NA
1_555
A
HOH
69
G
O
HOH
1_555
100.9
B
HOH
64
H
O
HOH
1_555
B
NA
52
F
NA
NA
1_555
A
HOH
69
G
O
HOH
1_555
85.2
A
LEU
40
A
O
LEU
29
1_555
A
NA
52
D
NA
NA
1_555
A
ASP
37
A
O
ASP
26
1_555
81.7
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
N
VAL
18
A
N
VAL
7
A
O
MET
27
A
O
MET
16
B
N
VAL
18
B
N
VAL
7
B
O
MET
27
B
O
MET
16
1
A
NA
52
D
NA
1
A
GLY
12
A
GLY
1
1
Y
1
A
SER
13
A
SER
2
1
Y
1
A
PRO
14
A
PRO
3
1
Y
1
A
GLU
15
A
GLU
4
1
Y
1
B
GLY
12
B
GLY
1
1
Y
1
B
SER
13
B
SER
2
1
Y
1
B
PRO
14
B
PRO
3
1
Y
1
A
GLN
24
82.53
-2.77
38.800
-0.48
0.00
0.00
0.96
0.00
-0.48
0.953
0.918
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.26151
0.21282
0.21526
1.90
23.77
175
3605
4.6
96.97
5.437
0.148
RANDOM
1
THROUGHOUT
SAD
0.175
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
1.90
23.77
16
423
4
0
403
0.014
0.021
412
1.584
1.938
558
5.328
5.000
49
48.557
25.238
21
17.483
15.000
70
15.208
15.000
2
0.100
0.200
61
0.006
0.021
320
0.897
1.500
259
1.683
2.000
420
2.688
3.000
153
4.484
4.500
138
0.325
0.337
1.950
15
247
20
90.97
32.4
1.90
100.0
3VHS
3816
0.063
1
21.3
5.5
97.6
0.384
1.90
1.93
3.3
187
1
3.5
89.5
data collection
ADSC
Quantum
phasing
SOLVE
refinement
REFMAC
5.5.0109
data reduction
HKL-2000
data scaling
HKL-2000
ATPase WRNIP1
Crystal structure of UBZ of human WRNIP1
1
N
N
1
N
N
2
N
N
3
N
N
2
N
N
3
N
N
4
N
N
4
N
N
A
HIS
31
A
HIS
20
HELX_P
A
LEU
40
A
LEU
29
1
1
10
B
ALA
29
B
ALA
18
HELX_P
B
LEU
36
B
LEU
25
1
2
8
disulf
2.027
A
CYS
39
A
SG
CYS
28
1_555
B
CYS
39
B
SG
CYS
28
1_555
metalc
1.989
A
HIS
35
A
NE2
HIS
24
1_555
A
ZN
51
C
ZN
ZN
1_555
metalc
2.011
A
HIS
31
A
NE2
HIS
20
1_555
B
ZN
51
E
ZN
ZN
1_555
metalc
2.078
B
HIS
35
B
NE2
HIS
24
1_555
B
ZN
51
E
ZN
ZN
1_555
metalc
2.090
A
MET
26
A
O
MET
15
1_555
B
NA
52
F
NA
NA
1_555
metalc
2.203
B
CYS
23
B
SG
CYS
12
1_555
B
ZN
51
E
ZN
ZN
1_555
metalc
2.247
B
CYS
20
B
SG
CYS
9
1_555
B
ZN
51
E
ZN
ZN
1_555
metalc
2.276
A
LEU
40
A
O
LEU
29
1_555
A
NA
52
D
NA
NA
1_555
metalc
2.309
A
ASP
37
A
O
ASP
26
1_555
A
NA
52
D
NA
NA
1_555
metalc
2.332
A
CYS
20
A
SG
CYS
9
1_555
A
ZN
51
C
ZN
ZN
1_555
metalc
2.352
A
CYS
23
A
SG
CYS
12
1_555
A
ZN
51
C
ZN
ZN
1_555
metalc
2.471
B
ASP
37
B
OD2
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
metalc
2.735
B
ASP
37
B
OD1
ASP
26
1_555
B
NA
52
F
NA
NA
1_555
metalc
1.929
B
NA
52
F
NA
NA
1_555
B
HOH
62
H
O
HOH
1_555
metalc
2.279
A
ZN
51
C
ZN
ZN
1_555
A
HOH
61
G
O
HOH
1_555
metalc
2.282
B
NA
52
F
NA
NA
1_555
B
HOH
64
H
O
HOH
1_555
metalc
2.507
B
NA
52
F
NA
NA
1_555
A
HOH
69
G
O
HOH
1_555
METAL BINDING PROTEIN
ZINC FINGER, UBIQUITIN-BINDING DOMAIN, UBIQUITIN BINDING, METAL BINDING PROTEIN
WRIP1_HUMAN
UNP
1
17
Q96S55
QVQCPVCQQMMPAAHINSHLDRCL
17
40
3VHS
17
40
Q96S55
A
1
6
29
17
40
3VHS
17
40
Q96S55
B
1
6
29
1
EXPRESSION TAG
GLY
12
3VHS
A
Q96S55
UNP
1
1
EXPRESSION TAG
SER
13
3VHS
A
Q96S55
UNP
2
1
EXPRESSION TAG
PRO
14
3VHS
A
Q96S55
UNP
3
1
EXPRESSION TAG
GLU
15
3VHS
A
Q96S55
UNP
4
1
EXPRESSION TAG
PHE
16
3VHS
A
Q96S55
UNP
5
2
EXPRESSION TAG
GLY
12
3VHS
B
Q96S55
UNP
1
2
EXPRESSION TAG
SER
13
3VHS
B
Q96S55
UNP
2
2
EXPRESSION TAG
PRO
14
3VHS
B
Q96S55
UNP
3
2
EXPRESSION TAG
GLU
15
3VHS
B
Q96S55
UNP
4
2
EXPRESSION TAG
PHE
16
3VHS
B
Q96S55
UNP
5
2
2
anti-parallel
anti-parallel
A
GLN
17
A
GLN
6
A
GLN
19
A
GLN
8
A
MET
26
A
MET
15
A
PRO
28
A
PRO
17
B
GLN
17
B
GLN
6
B
GLN
19
B
GLN
8
B
MET
26
B
MET
15
B
PRO
28
B
PRO
17
BINDING SITE FOR RESIDUE ZN A 51
Software
4
BINDING SITE FOR RESIDUE NA A 52
Software
6
BINDING SITE FOR RESIDUE ZN B 51
Software
4
BINDING SITE FOR RESIDUE NA B 52
Software
5
A
CYS
20
A
CYS
9
4
1_555
A
CYS
23
A
CYS
12
4
1_555
A
HIS
35
A
HIS
24
4
1_555
A
HOH
61
G
HOH
4
1_555
A
ASP
37
A
ASP
26
6
1_555
A
ASP
37
A
ASP
26
6
3_554
A
LEU
40
A
LEU
29
6
1_555
A
LEU
40
A
LEU
29
6
3_554
A
HOH
72
G
HOH
6
3_554
A
HOH
72
G
HOH
6
1_555
A
HIS
31
A
HIS
20
4
1_555
B
CYS
20
B
CYS
9
4
1_555
B
CYS
23
B
CYS
12
4
1_555
B
HIS
35
B
HIS
24
4
1_555
A
MET
26
A
MET
15
5
1_555
A
HOH
69
G
HOH
5
1_555
B
ASP
37
B
ASP
26
5
1_555
B
HOH
62
H
HOH
5
1_555
B
HOH
64
H
HOH
5
1_555
20
C 2 2 21