0.018302
0.000000
0.000000
0.000000
0.013472
0.000000
0.000000
0.000000
0.012564
0.00000
0.00000
0.00000
Shen, L.N.
Liu, H.
Dong, C.
Xirodimas, D.
Naismith, J.H.
Hay, R.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
54.638
74.226
79.590
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
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
UK
Embo J.
EMJODG
0897
0261-4189
24
1341
10.1038/SJ.EMBOJ.7600628
15775960
Structural Basis of Nedd8 Ubiquitin Discrimination by the Deneddylating Enzyme Nedp1
2005
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
CCD
2004-03-01
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.008
1.0
BM14
ESRF
1.008
SYNCHROTRON
ESRF BEAMLINE BM14
24073.164
SENTRIN-SPECIFIC PROTEASE 8
3.4.22.-
1
man
polymer
8661.055
NEDDYLIN
1
man
polymer
18.015
water
214
nat
water
NEDP1, SENTRIN/SUMO-SPECIFIC PROTEASE SENP8, CYSTEINE PROTEASE FKSG8, PROTEASE, CYSTEINE 2
NEDD8, UBIQUITIN-LIKE PROTEIN NEDD8
no
no
MDPVVLSYMDSLLRQSDVSLLDPPSWLNDHIIGFAFEYFANSQFHDSSDHVSFISPEVTQFIKCTSNPAEIAMFLEPLDL
PNKRVVFLAINDNSNQAAGGSHWSLLVYLQDKNSFFHYDSHSRSNSVHAKQVAEKLEAFLGRKGDKLAFVEEKAPAQQNS
YDCGMYVICNTEALCQNFFRQQTESLLQLLTPAYITKKRGEWKDLIATLAKK
MDPVVLSYMDSLLRQSDVSLLDPPSWLNDHIIGFAFEYFANSQFHDSSDHVSFISPEVTQFIKCTSNPAEIAMFLEPLDL
PNKRVVFLAINDNSNQAAGGSHWSLLVYLQDKNSFFHYDSHSRSNSVHAKQVAEKLEAFLGRKGDKLAFVEEKAPAQQNS
YDCGMYVICNTEALCQNFFRQQTESLLQLLTPAYITKKRGEWKDLIATLAKK
A
polypeptide(L)
no
no
SMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG
SMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG
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
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
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
HUMAN
sample
9606
HOMO SAPIENS
469008
ESCHERICHIA COLI
BL21(DE3)
PET
HUMAN
sample
9606
HOMO SAPIENS
469008
ESCHERICHIA COLI
BL21(DE3)
PET
1
2.30
46.10
4.50
CRYSTALS WERE GROWN BY SETTING-DROP METHOD BY MIXING THE NEDP1-NEDD8 COMPLEX (20MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 20%PEG8000, 200MM NACL, 100MM PHOSPHATE CITRATE PH4.5, pH 4.50
repository
Initial release
Advisory
Version format compliance
1
0
2005-09-15
1
1
2011-07-13
STRUCTURE OF NEDD8
APPBP1-UBA3-NEDD8, AN E1-UBIQUITIN-LIKE PROTEIN COMPLEX
APPBP1-UBA3-NEDD8, AN E1-UBIQUITIN-LIKE PROTEIN COMPLEXWITH ATP
CRYSTAL STRUCTURE OF DEN1 IN COMPLEX WITH NEDD8
NEDD8 PROTEASE
PDBE
Y
PDBE
2005-02-18
REL
1
A
O
HOH
2006
7.86
1
A
O
HOH
2015
6.19
1
B
O
HOH
2009
6.12
HOH
water
FUNCTION: POSSIBLE INVOLVEMENT IN THE RELEASE OF SENTRINS.
POSSIBLE ROLE DURING THE EMBRYONIC DEVELOPMENT AND
DIFFERENTIATION OF THE CENTRAL NERVOUS SYSTEM
EXTRA N-TERMINAL RESIDUE FROM CLONING SER FOR CHAIN B.
THE ORIGINAL SAMPLE FOR CHAIN B CONTAINS 82 RESIDUES
INCLUDING GLY GLY LEU ARG GLN (77-81) BUT THESE RESIDUES
ARE CLEAVED OFF BY THE PROTEASE DURING THE COMPLEX
FORMATION. THESE RESIDUES ARE NOT THEREFORE PART OF
OF THE CRYSTALLIZED COMPLEX.
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
HOH
2027
3
HOH
HOH
2027
A
HOH
2028
3
HOH
HOH
2028
A
HOH
2029
3
HOH
HOH
2029
A
HOH
2030
3
HOH
HOH
2030
A
HOH
2031
3
HOH
HOH
2031
A
HOH
2032
3
HOH
HOH
2032
A
HOH
2033
3
HOH
HOH
2033
A
HOH
2034
3
HOH
HOH
2034
A
HOH
2035
3
HOH
HOH
2035
A
HOH
2036
3
HOH
HOH
2036
A
HOH
2037
3
HOH
HOH
2037
A
HOH
2038
3
HOH
HOH
2038
A
HOH
2039
3
HOH
HOH
2039
A
HOH
2040
3
HOH
HOH
2040
A
HOH
2041
3
HOH
HOH
2041
A
HOH
2042
3
HOH
HOH
2042
A
HOH
2043
3
HOH
HOH
2043
A
HOH
2044
3
HOH
HOH
2044
A
HOH
2045
3
HOH
HOH
2045
A
HOH
2046
3
HOH
HOH
2046
A
HOH
2047
3
HOH
HOH
2047
A
HOH
2048
3
HOH
HOH
2048
A
HOH
2049
3
HOH
HOH
2049
A
HOH
2050
3
HOH
HOH
2050
A
HOH
2051
3
HOH
HOH
2051
A
HOH
2052
3
HOH
HOH
2052
A
HOH
2053
3
HOH
HOH
2053
A
HOH
2054
3
HOH
HOH
2054
A
HOH
2055
3
HOH
HOH
2055
A
HOH
2056
3
HOH
HOH
2056
A
HOH
2057
3
HOH
HOH
2057
A
HOH
2058
3
HOH
HOH
2058
A
HOH
2059
3
HOH
HOH
2059
A
HOH
2060
3
HOH
HOH
2060
A
HOH
2061
3
HOH
HOH
2061
A
HOH
2062
3
HOH
HOH
2062
A
HOH
2063
3
HOH
HOH
2063
A
HOH
2064
3
HOH
HOH
2064
A
HOH
2065
3
HOH
HOH
2065
A
HOH
2066
3
HOH
HOH
2066
A
HOH
2067
3
HOH
HOH
2067
A
HOH
2068
3
HOH
HOH
2068
A
HOH
2069
3
HOH
HOH
2069
A
HOH
2070
3
HOH
HOH
2070
A
HOH
2071
3
HOH
HOH
2071
A
HOH
2072
3
HOH
HOH
2072
A
HOH
2073
3
HOH
HOH
2073
A
HOH
2074
3
HOH
HOH
2074
A
HOH
2075
3
HOH
HOH
2075
A
HOH
2076
3
HOH
HOH
2076
A
HOH
2077
3
HOH
HOH
2077
A
HOH
2078
3
HOH
HOH
2078
A
HOH
2079
3
HOH
HOH
2079
A
HOH
2080
3
HOH
HOH
2080
A
HOH
2081
3
HOH
HOH
2081
A
HOH
2082
3
HOH
HOH
2082
A
HOH
2083
3
HOH
HOH
2083
A
HOH
2084
3
HOH
HOH
2084
A
HOH
2085
3
HOH
HOH
2085
A
HOH
2086
3
HOH
HOH
2086
A
HOH
2087
3
HOH
HOH
2087
A
HOH
2088
3
HOH
HOH
2088
A
HOH
2089
3
HOH
HOH
2089
A
HOH
2090
3
HOH
HOH
2090
A
HOH
2091
3
HOH
HOH
2091
A
HOH
2092
3
HOH
HOH
2092
A
HOH
2093
3
HOH
HOH
2093
A
HOH
2094
3
HOH
HOH
2094
A
HOH
2095
3
HOH
HOH
2095
A
HOH
2096
3
HOH
HOH
2096
A
HOH
2097
3
HOH
HOH
2097
A
HOH
2098
3
HOH
HOH
2098
A
HOH
2099
3
HOH
HOH
2099
A
HOH
2100
3
HOH
HOH
2100
A
HOH
2101
3
HOH
HOH
2101
A
HOH
2102
3
HOH
HOH
2102
A
HOH
2103
3
HOH
HOH
2103
A
HOH
2104
3
HOH
HOH
2104
A
HOH
2105
3
HOH
HOH
2105
A
HOH
2106
3
HOH
HOH
2106
A
HOH
2107
3
HOH
HOH
2107
A
HOH
2108
3
HOH
HOH
2108
A
HOH
2109
3
HOH
HOH
2109
A
HOH
2110
3
HOH
HOH
2110
A
HOH
2111
3
HOH
HOH
2111
A
HOH
2112
3
HOH
HOH
2112
A
HOH
2113
3
HOH
HOH
2113
A
HOH
2114
3
HOH
HOH
2114
A
HOH
2115
3
HOH
HOH
2115
A
HOH
2116
3
HOH
HOH
2116
A
HOH
2117
3
HOH
HOH
2117
A
HOH
2118
3
HOH
HOH
2118
A
HOH
2119
3
HOH
HOH
2119
A
HOH
2120
3
HOH
HOH
2120
A
HOH
2121
3
HOH
HOH
2121
A
HOH
2122
3
HOH
HOH
2122
A
HOH
2123
3
HOH
HOH
2123
A
HOH
2124
3
HOH
HOH
2124
A
HOH
2125
3
HOH
HOH
2125
A
HOH
2126
3
HOH
HOH
2126
A
HOH
2127
3
HOH
HOH
2127
A
HOH
2128
3
HOH
HOH
2128
A
HOH
2129
3
HOH
HOH
2129
A
HOH
2130
3
HOH
HOH
2130
A
HOH
2131
3
HOH
HOH
2131
A
HOH
2132
3
HOH
HOH
2132
A
HOH
2133
3
HOH
HOH
2133
A
HOH
2134
3
HOH
HOH
2134
A
HOH
2135
3
HOH
HOH
2135
A
HOH
2136
3
HOH
HOH
2136
A
HOH
2137
3
HOH
HOH
2137
A
HOH
2138
3
HOH
HOH
2138
A
HOH
2139
3
HOH
HOH
2139
A
HOH
2140
3
HOH
HOH
2140
A
HOH
2141
3
HOH
HOH
2141
A
HOH
2142
3
HOH
HOH
2142
A
HOH
2143
3
HOH
HOH
2143
A
HOH
2144
3
HOH
HOH
2144
A
HOH
2145
3
HOH
HOH
2145
A
HOH
2146
3
HOH
HOH
2146
A
HOH
2147
3
HOH
HOH
2147
A
HOH
2148
3
HOH
HOH
2148
A
HOH
2001
3
HOH
HOH
2001
B
HOH
2002
3
HOH
HOH
2002
B
HOH
2003
3
HOH
HOH
2003
B
HOH
2004
3
HOH
HOH
2004
B
HOH
2005
3
HOH
HOH
2005
B
HOH
2006
3
HOH
HOH
2006
B
HOH
2007
3
HOH
HOH
2007
B
HOH
2008
3
HOH
HOH
2008
B
HOH
2009
3
HOH
HOH
2009
B
HOH
2010
3
HOH
HOH
2010
B
HOH
2011
3
HOH
HOH
2011
B
HOH
2012
3
HOH
HOH
2012
B
HOH
2013
3
HOH
HOH
2013
B
HOH
2014
3
HOH
HOH
2014
B
HOH
2015
3
HOH
HOH
2015
B
HOH
2016
3
HOH
HOH
2016
B
HOH
2017
3
HOH
HOH
2017
B
HOH
2018
3
HOH
HOH
2018
B
HOH
2019
3
HOH
HOH
2019
B
HOH
2020
3
HOH
HOH
2020
B
HOH
2021
3
HOH
HOH
2021
B
HOH
2022
3
HOH
HOH
2022
B
HOH
2023
3
HOH
HOH
2023
B
HOH
2024
3
HOH
HOH
2024
B
HOH
2025
3
HOH
HOH
2025
B
HOH
2026
3
HOH
HOH
2026
B
HOH
2027
3
HOH
HOH
2027
B
HOH
2028
3
HOH
HOH
2028
B
HOH
2029
3
HOH
HOH
2029
B
HOH
2030
3
HOH
HOH
2030
B
HOH
2031
3
HOH
HOH
2031
B
HOH
2032
3
HOH
HOH
2032
B
HOH
2033
3
HOH
HOH
2033
B
HOH
2034
3
HOH
HOH
2034
B
HOH
2035
3
HOH
HOH
2035
B
HOH
2036
3
HOH
HOH
2036
B
HOH
2037
3
HOH
HOH
2037
B
HOH
2038
3
HOH
HOH
2038
B
HOH
2039
3
HOH
HOH
2039
B
HOH
2040
3
HOH
HOH
2040
B
HOH
2041
3
HOH
HOH
2041
B
HOH
2042
3
HOH
HOH
2042
B
HOH
2043
3
HOH
HOH
2043
B
HOH
2044
3
HOH
HOH
2044
B
HOH
2045
3
HOH
HOH
2045
B
HOH
2046
3
HOH
HOH
2046
B
HOH
2047
3
HOH
HOH
2047
B
HOH
2048
3
HOH
HOH
2048
B
HOH
2049
3
HOH
HOH
2049
B
HOH
2050
3
HOH
HOH
2050
B
HOH
2051
3
HOH
HOH
2051
B
HOH
2052
3
HOH
HOH
2052
B
HOH
2053
3
HOH
HOH
2053
B
HOH
2054
3
HOH
HOH
2054
B
HOH
2055
3
HOH
HOH
2055
B
HOH
2056
3
HOH
HOH
2056
B
HOH
2057
3
HOH
HOH
2057
B
HOH
2058
3
HOH
HOH
2058
B
HOH
2059
3
HOH
HOH
2059
B
HOH
2060
3
HOH
HOH
2060
B
HOH
2061
3
HOH
HOH
2061
B
HOH
2062
3
HOH
HOH
2062
B
HOH
2063
3
HOH
HOH
2063
B
HOH
2064
3
HOH
HOH
2064
B
HOH
2065
3
HOH
HOH
2065
B
HOH
2066
3
HOH
HOH
2066
B
MET
1
n
1
MET
1
A
ASP
2
n
2
ASP
2
A
PRO
3
n
3
PRO
3
A
VAL
4
n
4
VAL
4
A
VAL
5
n
5
VAL
5
A
LEU
6
n
6
LEU
6
A
SER
7
n
7
SER
7
A
TYR
8
n
8
TYR
8
A
MET
9
n
9
MET
9
A
ASP
10
n
10
ASP
10
A
SER
11
n
11
SER
11
A
LEU
12
n
12
LEU
12
A
LEU
13
n
13
LEU
13
A
ARG
14
n
14
ARG
14
A
GLN
15
n
15
GLN
15
A
SER
16
n
16
SER
16
A
ASP
17
n
17
ASP
17
A
VAL
18
n
18
VAL
18
A
SER
19
n
19
SER
19
A
LEU
20
n
20
LEU
20
A
LEU
21
n
21
LEU
21
A
ASP
22
n
22
ASP
22
A
PRO
23
n
23
PRO
23
A
PRO
24
n
24
PRO
24
A
SER
25
n
25
SER
25
A
TRP
26
n
26
TRP
26
A
LEU
27
n
27
LEU
27
A
ASN
28
n
28
ASN
28
A
ASP
29
n
29
ASP
29
A
HIS
30
n
30
HIS
30
A
ILE
31
n
31
ILE
31
A
ILE
32
n
32
ILE
32
A
GLY
33
n
33
GLY
33
A
PHE
34
n
34
PHE
34
A
ALA
35
n
35
ALA
35
A
PHE
36
n
36
PHE
36
A
GLU
37
n
37
GLU
37
A
TYR
38
n
38
TYR
38
A
PHE
39
n
39
PHE
39
A
ALA
40
n
40
ALA
40
A
ASN
41
n
41
ASN
41
A
SER
42
n
42
SER
42
A
GLN
43
n
43
GLN
43
A
PHE
44
n
44
PHE
44
A
HIS
45
n
45
HIS
45
A
ASP
46
n
46
ASP
46
A
SER
47
n
47
SER
47
A
SER
48
n
48
SER
48
A
ASP
49
n
49
ASP
49
A
HIS
50
n
50
HIS
50
A
VAL
51
n
51
VAL
51
A
SER
52
n
52
SER
52
A
PHE
53
n
53
PHE
53
A
ILE
54
n
54
ILE
54
A
SER
55
n
55
SER
55
A
PRO
56
n
56
PRO
56
A
GLU
57
n
57
GLU
57
A
VAL
58
n
58
VAL
58
A
THR
59
n
59
THR
59
A
GLN
60
n
60
GLN
60
A
PHE
61
n
61
PHE
61
A
ILE
62
n
62
ILE
62
A
LYS
63
n
63
LYS
63
A
CYS
64
n
64
CYS
64
A
THR
65
n
65
THR
65
A
SER
66
n
66
SER
66
A
ASN
67
n
67
ASN
67
A
PRO
68
n
68
PRO
68
A
ALA
69
n
69
ALA
69
A
GLU
70
n
70
GLU
70
A
ILE
71
n
71
ILE
71
A
ALA
72
n
72
ALA
72
A
MET
73
n
73
MET
73
A
PHE
74
n
74
PHE
74
A
LEU
75
n
75
LEU
75
A
GLU
76
n
76
GLU
76
A
PRO
77
n
77
PRO
77
A
LEU
78
n
78
LEU
78
A
ASP
79
n
79
ASP
79
A
LEU
80
n
80
LEU
80
A
PRO
81
n
81
PRO
81
A
ASN
82
n
82
ASN
82
A
LYS
83
n
83
LYS
83
A
ARG
84
n
84
ARG
84
A
VAL
85
n
85
VAL
85
A
VAL
86
n
86
VAL
86
A
PHE
87
n
87
PHE
87
A
LEU
88
n
88
LEU
88
A
ALA
89
n
89
ALA
89
A
ILE
90
n
90
ILE
90
A
ASN
91
n
91
ASN
91
A
ASP
92
n
92
ASP
92
A
ASN
93
n
93
ASN
93
A
SER
94
n
94
SER
94
A
ASN
95
n
95
ASN
95
A
GLN
96
n
96
GLN
96
A
ALA
97
n
97
ALA
97
A
ALA
98
n
98
ALA
98
A
GLY
99
n
99
GLY
99
A
GLY
100
n
100
GLY
100
A
SER
101
n
101
SER
101
A
HIS
102
n
102
HIS
102
A
TRP
103
n
103
TRP
103
A
SER
104
n
104
SER
104
A
LEU
105
n
105
LEU
105
A
LEU
106
n
106
LEU
106
A
VAL
107
n
107
VAL
107
A
TYR
108
n
108
TYR
108
A
LEU
109
n
109
LEU
109
A
GLN
110
n
110
GLN
110
A
ASP
111
n
111
ASP
111
A
LYS
112
n
112
LYS
112
A
ASN
113
n
113
ASN
113
A
SER
114
n
114
SER
114
A
PHE
115
n
115
PHE
115
A
PHE
116
n
116
PHE
116
A
HIS
117
n
117
HIS
117
A
TYR
118
n
118
TYR
118
A
ASP
119
n
119
ASP
119
A
SER
120
n
120
SER
120
A
HIS
121
n
121
HIS
121
A
SER
122
n
122
SER
122
A
ARG
123
n
123
ARG
123
A
SER
124
n
124
SER
124
A
ASN
125
n
125
ASN
125
A
SER
126
n
126
SER
126
A
VAL
127
n
127
VAL
127
A
HIS
128
n
128
HIS
128
A
ALA
129
n
129
ALA
129
A
LYS
130
n
130
LYS
130
A
GLN
131
n
131
GLN
131
A
VAL
132
n
132
VAL
132
A
ALA
133
n
133
ALA
133
A
GLU
134
n
134
GLU
134
A
LYS
135
n
135
LYS
135
A
LEU
136
n
136
LEU
136
A
GLU
137
n
137
GLU
137
A
ALA
138
n
138
ALA
138
A
PHE
139
n
139
PHE
139
A
LEU
140
n
140
LEU
140
A
GLY
141
n
141
GLY
141
A
ARG
142
n
142
ARG
142
A
LYS
143
n
143
LYS
143
A
GLY
144
n
144
GLY
144
A
ASP
145
n
145
ASP
145
A
LYS
146
n
146
LYS
146
A
LEU
147
n
147
LEU
147
A
ALA
148
n
148
ALA
148
A
PHE
149
n
149
PHE
149
A
VAL
150
n
150
VAL
150
A
GLU
151
n
151
GLU
151
A
GLU
152
n
152
GLU
152
A
LYS
153
n
153
LYS
153
A
ALA
154
n
154
ALA
154
A
PRO
155
n
155
PRO
155
A
ALA
156
n
156
ALA
156
A
GLN
157
n
157
GLN
157
A
GLN
158
n
158
GLN
158
A
ASN
159
n
159
ASN
159
A
SER
160
n
160
SER
160
A
TYR
161
n
161
TYR
161
A
ASP
162
n
162
ASP
162
A
CYS
163
n
163
CYS
163
A
GLY
164
n
164
GLY
164
A
MET
165
n
165
MET
165
A
TYR
166
n
166
TYR
166
A
VAL
167
n
167
VAL
167
A
ILE
168
n
168
ILE
168
A
CYS
169
n
169
CYS
169
A
ASN
170
n
170
ASN
170
A
THR
171
n
171
THR
171
A
GLU
172
n
172
GLU
172
A
ALA
173
n
173
ALA
173
A
LEU
174
n
174
LEU
174
A
CYS
175
n
175
CYS
175
A
GLN
176
n
176
GLN
176
A
ASN
177
n
177
ASN
177
A
PHE
178
n
178
PHE
178
A
PHE
179
n
179
PHE
179
A
ARG
180
n
180
ARG
180
A
GLN
181
n
181
GLN
181
A
GLN
182
n
182
GLN
182
A
THR
183
n
183
THR
183
A
GLU
184
n
184
GLU
184
A
SER
185
n
185
SER
185
A
LEU
186
n
186
LEU
186
A
LEU
187
n
187
LEU
187
A
GLN
188
n
188
GLN
188
A
LEU
189
n
189
LEU
189
A
LEU
190
n
190
LEU
190
A
THR
191
n
191
THR
191
A
PRO
192
n
192
PRO
192
A
ALA
193
n
193
ALA
193
A
TYR
194
n
194
TYR
194
A
ILE
195
n
195
ILE
195
A
THR
196
n
196
THR
196
A
LYS
197
n
197
LYS
197
A
LYS
198
n
198
LYS
198
A
ARG
199
n
199
ARG
199
A
GLY
200
n
200
GLY
200
A
GLU
201
n
201
GLU
201
A
TRP
202
n
202
TRP
202
A
LYS
203
n
203
LYS
203
A
ASP
204
n
204
ASP
204
A
LEU
205
n
205
LEU
205
A
ILE
206
n
206
ILE
206
A
ALA
207
n
207
ALA
207
A
THR
208
n
208
THR
208
A
LEU
209
n
209
LEU
209
A
ALA
210
n
210
ALA
210
A
LYS
211
n
211
LYS
211
A
LYS
212
n
212
LYS
212
A
SER
0
n
1
SER
0
B
MET
1
n
2
MET
1
B
LEU
2
n
3
LEU
2
B
ILE
3
n
4
ILE
3
B
LYS
4
n
5
LYS
4
B
VAL
5
n
6
VAL
5
B
LYS
6
n
7
LYS
6
B
THR
7
n
8
THR
7
B
LEU
8
n
9
LEU
8
B
THR
9
n
10
THR
9
B
GLY
10
n
11
GLY
10
B
LYS
11
n
12
LYS
11
B
GLU
12
n
13
GLU
12
B
ILE
13
n
14
ILE
13
B
GLU
14
n
15
GLU
14
B
ILE
15
n
16
ILE
15
B
ASP
16
n
17
ASP
16
B
ILE
17
n
18
ILE
17
B
GLU
18
n
19
GLU
18
B
PRO
19
n
20
PRO
19
B
THR
20
n
21
THR
20
B
ASP
21
n
22
ASP
21
B
LYS
22
n
23
LYS
22
B
VAL
23
n
24
VAL
23
B
GLU
24
n
25
GLU
24
B
ARG
25
n
26
ARG
25
B
ILE
26
n
27
ILE
26
B
LYS
27
n
28
LYS
27
B
GLU
28
n
29
GLU
28
B
ARG
29
n
30
ARG
29
B
VAL
30
n
31
VAL
30
B
GLU
31
n
32
GLU
31
B
GLU
32
n
33
GLU
32
B
LYS
33
n
34
LYS
33
B
GLU
34
n
35
GLU
34
B
GLY
35
n
36
GLY
35
B
ILE
36
n
37
ILE
36
B
PRO
37
n
38
PRO
37
B
PRO
38
n
39
PRO
38
B
GLN
39
n
40
GLN
39
B
GLN
40
n
41
GLN
40
B
GLN
41
n
42
GLN
41
B
ARG
42
n
43
ARG
42
B
LEU
43
n
44
LEU
43
B
ILE
44
n
45
ILE
44
B
TYR
45
n
46
TYR
45
B
SER
46
n
47
SER
46
B
GLY
47
n
48
GLY
47
B
LYS
48
n
49
LYS
48
B
GLN
49
n
50
GLN
49
B
MET
50
n
51
MET
50
B
ASN
51
n
52
ASN
51
B
ASP
52
n
53
ASP
52
B
GLU
53
n
54
GLU
53
B
LYS
54
n
55
LYS
54
B
THR
55
n
56
THR
55
B
ALA
56
n
57
ALA
56
B
ALA
57
n
58
ALA
57
B
ASP
58
n
59
ASP
58
B
TYR
59
n
60
TYR
59
B
LYS
60
n
61
LYS
60
B
ILE
61
n
62
ILE
61
B
LEU
62
n
63
LEU
62
B
GLY
63
n
64
GLY
63
B
GLY
64
n
65
GLY
64
B
SER
65
n
66
SER
65
B
VAL
66
n
67
VAL
66
B
LEU
67
n
68
LEU
67
B
HIS
68
n
69
HIS
68
B
LEU
69
n
70
LEU
69
B
VAL
70
n
71
VAL
70
B
LEU
71
n
72
LEU
71
B
ALA
72
n
73
ALA
72
B
LEU
73
n
74
LEU
73
B
ARG
74
n
75
ARG
74
B
GLY
75
n
76
GLY
75
B
GLY
76
n
77
GLY
76
B
1.4071
-0.2885
-0.1800
1.9757
-0.3739
1.3367
-0.0058
-0.0667
0.0545
0.0272
0.0539
-0.1012
-0.1042
0.0333
-0.0481
-0.1043
-0.0264
0.0024
-0.1385
-0.0251
0.0981
refined
26.0310
5.2140
23.5150
X-RAY DIFFRACTION
4.9434
-0.2712
-1.4175
1.0171
0.0739
1.9424
-0.1091
-0.0614
-0.4003
0.0783
0.0086
0.1594
0.0310
-0.2071
0.1005
-0.1357
-0.0268
-0.0039
-0.1171
0.0279
0.1482
refined
5.7210
-2.3330
30.1930
X-RAY DIFFRACTION
A
1
A
211
X-RAY DIFFRACTION
1
B
1
B
76
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
2
dimeric
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
TYR
8
A
N
TYR
8
A
O
SER
11
A
O
SER
11
A
N
SER
52
A
N
SER
52
A
O
VAL
85
A
O
VAL
85
A
N
ILE
90
A
N
ILE
90
A
O
SER
104
A
O
SER
104
A
N
LEU
109
A
N
LEU
109
A
O
SER
114
A
O
SER
114
A
N
HIS
117
A
N
HIS
117
A
O
VAL
150
A
O
VAL
150
B
N
ILE
17
B
N
ILE
18
B
O
MET
1
B
O
MET
2
B
N
LYS
6
B
N
LYS
7
B
O
LEU
67
B
O
LEU
68
B
N
VAL
70
B
N
VAL
71
B
O
ARG
42
B
O
ARG
43
B
N
TYR
45
B
N
TYR
46
B
O
LYS
48
B
O
LYS
49
1
A
CG
MET
1
A
CG
MET
1
1
Y
1
A
SD
MET
1
A
SD
MET
1
1
Y
1
A
CE
MET
1
A
CE
MET
1
1
Y
1
A
CD
GLU
76
A
CD
GLU
76
1
Y
1
A
OE1
GLU
76
A
OE1
GLU
76
1
Y
1
A
OE2
GLU
76
A
OE2
GLU
76
1
Y
1
A
CE
LYS
130
A
CE
LYS
130
1
Y
1
A
NZ
LYS
130
A
NZ
LYS
130
1
Y
1
A
NE
ARG
142
A
NE
ARG
142
1
Y
1
A
CZ
ARG
142
A
CZ
ARG
142
1
Y
1
A
NH1
ARG
142
A
NH1
ARG
142
1
Y
1
A
NH2
ARG
142
A
NH2
ARG
142
1
Y
1
A
CG
LYS
143
A
CG
LYS
143
1
Y
1
A
CD
LYS
143
A
CD
LYS
143
1
Y
1
A
CE
LYS
143
A
CE
LYS
143
1
Y
1
A
NZ
LYS
143
A
NZ
LYS
143
1
Y
1
A
CG
LYS
146
A
CG
LYS
146
1
Y
1
A
CD
LYS
146
A
CD
LYS
146
1
Y
1
A
CE
LYS
146
A
CE
LYS
146
1
Y
1
A
CD
LYS
153
A
CD
LYS
153
1
Y
1
A
CE
LYS
153
A
CE
LYS
153
1
Y
1
A
NZ
LYS
153
A
NZ
LYS
153
1
Y
1
A
CD
GLN
181
A
CD
GLN
181
1
Y
1
A
OE1
GLN
181
A
OE1
GLN
181
1
Y
1
A
NE2
GLN
181
A
NE2
GLN
181
1
Y
1
A
CD
GLN
188
A
CD
GLN
188
1
Y
1
A
OE1
GLN
188
A
OE1
GLN
188
1
Y
1
A
NE2
GLN
188
A
NE2
GLN
188
1
Y
1
A
CD
LYS
211
A
CD
LYS
211
1
Y
1
A
CE
LYS
211
A
CE
LYS
211
1
Y
1
A
NZ
LYS
211
A
NZ
LYS
211
1
Y
1
A
CA
LYS
212
A
CA
LYS
212
1
Y
1
A
C
LYS
212
A
C
LYS
212
1
Y
1
A
O
LYS
212
A
O
LYS
212
1
Y
1
A
CB
LYS
212
A
CB
LYS
212
1
Y
1
A
CG
LYS
212
A
CG
LYS
212
1
Y
1
A
CD
LYS
212
A
CD
LYS
212
1
Y
1
A
CE
LYS
212
A
CE
LYS
212
1
Y
1
A
NZ
LYS
212
A
NZ
LYS
212
1
Y
1
B
CE
LYS
4
B
CE
LYS
5
1
Y
1
B
NZ
LYS
4
B
NZ
LYS
5
1
Y
1
B
CD
LYS
11
B
CD
LYS
12
1
Y
1
B
CE
LYS
11
B
CE
LYS
12
1
Y
1
B
NZ
LYS
11
B
NZ
LYS
12
1
Y
1
B
CD
GLU
24
B
CD
GLU
25
1
Y
1
B
OE1
GLU
24
B
OE1
GLU
25
1
Y
1
B
OE2
GLU
24
B
OE2
GLU
25
1
Y
1
B
CD
LYS
60
B
CD
LYS
61
1
Y
1
B
CE
LYS
60
B
CE
LYS
61
1
Y
1
B
NZ
LYS
60
B
NZ
LYS
61
1
Y
1
A
B
SG
C
CYS
GLY
163
76
1.76
1
A
A
O
O
HOH
HOH
2121
2124
1.93
1
B
B
N
O
SER
HOH
0
2001
2.03
1
A
A
O
O
HOH
HOH
2007
2008
2.14
1
A
A
O
O
HOH
HOH
2033
2083
2.17
1
5.70
0.90
118.30
124.00
A
A
A
CB
CG
OD2
ASP
ASP
ASP
79
79
79
N
1
6.56
0.90
118.30
124.86
A
A
A
CB
CG
OD2
ASP
ASP
ASP
162
162
162
N
1
8.82
0.50
120.30
129.12
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
42
42
42
N
1
-9.75
0.50
120.30
110.55
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
42
42
42
N
1
A
B
O
O
HOH
HOH
2033
2024
2.18
1_555
3_655
1
A
MET
9
52.72
-123.04
1
A
SER
42
-124.77
-66.04
1
A
SER
122
-38.04
123.19
23.91
-0.37000
0.00000
0.00000
1.18000
0.00000
-0.81000
0.960
0.937
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
0.209
0.169
0.171
1.90
54.23
1307
24174
5.100
97.8
6.177
0.092
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MAD
0.137
0.130
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
1.90
54.23
214
2464
0
0
2250
0.017
0.022
2297
1.569
1.945
3113
5.679
5.000
286
36.274
25.094
106
14.120
15.000
389
21.851
15.000
9
0.109
0.200
350
0.007
0.020
1741
0.203
0.200
1053
0.311
0.200
1603
0.196
0.200
184
0.218
0.200
33
0.309
0.200
16
1.099
1.500
1477
1.616
2.000
2316
3.018
3.000
927
4.439
4.500
797
0.2410
0.2000
1.95
76
1423
20
1.900
54.000
2BKR
25411
0.000
0.08000
1
5.5000
6.900
97.8
0.45000
1.90
1.95
3.000
1
3.00
83.7
refinement
REFMAC
5.2.0003
data reduction
MOSFLM
data scaling
SCALA
phasing
SOLVE
SENTRIN-SPECIFIC PROTEASE 8 (E.C.3.4.22.-), NEDDYLIN
NEDD8 NEDP1 complex
1
N
N
2
N
N
3
N
N
3
N
N
A
GLN
15
A
GLN
15
HELX_P
A
LEU
20
A
LEU
20
1
1
6
A
ASN
28
A
ASN
28
HELX_P
A
SER
42
A
SER
42
1
2
15
A
PHE
44
A
PHE
44
HELX_P
A
SER
48
A
SER
48
5
3
5
A
SER
55
A
SER
55
HELX_P
A
THR
65
A
THR
65
1
4
11
A
ASN
67
A
ASN
67
HELX_P
A
GLU
76
A
GLU
76
1
5
10
A
PRO
77
A
PRO
77
HELX_P
A
LYS
83
A
LYS
83
5
6
7
A
ASP
111
A
ASP
111
HELX_P
A
ASN
113
A
ASN
113
5
7
3
A
ASN
125
A
ASN
125
HELX_P
A
GLY
141
A
GLY
141
1
8
17
A
ASP
162
A
ASP
162
HELX_P
A
ARG
180
A
ARG
180
1
9
19
A
SER
185
A
SER
185
HELX_P
A
LEU
190
A
LEU
190
1
10
6
A
THR
191
A
THR
191
HELX_P
A
LYS
211
A
LYS
211
1
11
21
B
LYS
22
B
LYS
23
HELX_P
B
GLY
35
B
GLY
36
1
12
14
B
PRO
37
B
PRO
38
HELX_P
B
GLN
39
B
GLN
40
5
13
3
PROTEIN-BINDING/HYDROLASE
PROTEIN-BINDING-HYDROLASE COMPLEX, UBIQUITIN, HYDROLASE, PROTEASE, THIOL PROTEASE, UBL CONJUGATION PATHWAY, UBIQUITIN-HYDROLASE COMPLEX
A
PRO
23
A
PRO
23
1
A
PRO
24
A
PRO
24
5.80
SENP8_HUMAN
UNP
1
Q96LD8
2BKR
PDB
2
2BKR
NEDD8_HUMAN
UNP
2
Q15843
1
212
2BKR
1
212
Q96LD8
A
1
1
212
0
0
2BKR
0
0
2BKR
B
2
1
1
1
76
2BKR
1
76
Q15843
B
3
2
77
1
CYS
conflict
SER
47
2BKR
A
Q96LD8
UNP
47
47
1
THR
conflict
SER
101
2BKR
A
Q96LD8
UNP
101
101
2
5
5
anti-parallel
parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
VAL
4
A
VAL
4
A
TYR
8
A
TYR
8
A
SER
11
A
SER
11
A
ARG
14
A
ARG
14
A
VAL
51
A
VAL
51
A
ILE
54
A
ILE
54
A
VAL
85
A
VAL
85
A
ASN
91
A
ASN
91
A
TRP
103
A
TRP
103
A
LEU
109
A
LEU
109
A
SER
114
A
SER
114
A
TYR
118
A
TYR
118
A
PHE
149
A
PHE
149
A
GLU
151
A
GLU
151
B
GLU
12
B
GLU
13
B
ILE
17
B
ILE
18
B
MET
1
B
MET
2
B
THR
7
B
THR
8
B
VAL
66
B
VAL
67
B
LEU
71
B
LEU
72
B
GLN
41
B
GLN
42
B
TYR
45
B
TYR
46
B
LYS
48
B
LYS
49
B
GLN
49
B
GLN
50
19
P 21 21 21