0.007999
0.000000
0.007537
0.000000
0.013881
0.000000
0.000000
0.000000
0.013087
0.00000
0.00000
0.00000
Pedelacq, J.D.
Waldo, G.S.
Cabantous, S.
Liong, E.C.
Berendzen, J.
Terwilliger, T.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
133.30
90.00
125.022
72.041
104.993
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
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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
C6 H14 O4
150.173
TRIETHYLENE GLYCOL
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
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C4 H12 N O3 1
122.143
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
non-polymer
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Protein Sci.
PRCIEI
0795
0961-8368
14
2562
2573
10.1110/ps.051664205
16195547
Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum
2005
10.2210/pdb1xqi/pdb
pdb_00001xqi
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
mirrors
CCD
2000-10-04
ADSC QUANTUM 4
Si 111 double crystal
MAD
M
x-ray
1
0.9792
1.0
0.9791
1.0
0.9500
1.0
X8C
NSLS
0.9792, 0.9791, 0.9500
SYNCHROTRON
NSLS BEAMLINE X8C
22029.693
Nucleoside diphosphate kinase
2.7.4.6
A10D, G33D, E40K, R71Q, S107N, I117N
3
man
polymer
122.143
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3
syn
non-polymer
150.173
TRIETHYLENE GLYCOL
3
syn
non-polymer
18.015
water
158
nat
water
NDK, NDP kinase, Nucleoside-2-P kinase
no
yes
(MSE)HAINIAFFDLI(MSE)PVEKTLLILKPDAVARGLVDEIISRFKKAGLKIVALK(MSE)VKASPEEIERFYPSSEE
WLQSAGQKLLKAYQELGIDPRAKIGTDDPVEVGRIIKRNLVKY(MSE)TSGPNVV(MSE)VLKGNRAVEIVRKLVGPTSP
HSAPPGTIRGDYSIDSPDLAAEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE
MHAINIAFFDLIMPVEKTLLILKPDAVARGLVDEIISRFKKAGLKIVALKMVKASPEEIERFYPSSEEWLQSAGQKLLKA
YQELGIDPRAKIGTDDPVEVGRIIKRNLVKYMTSGPNVVMVLKGNRAVEIVRKLVGPTSPHSAPPGTIRGDYSIDSPDLA
AEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE
A,B,C
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
Pyrobaculum
STRAIN IM2 DSM 7523 ATCC 51768
Escherichia
Escherichia coli
sample
ndk
13773
Pyrobaculum aerophilum
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
modified pET 28 C-6HIS
1
2.65
53.2
VAPOR DIFFUSION, HANGING DROP
8.5
PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2005-09-20
1
1
2008-04-30
1
2
2011-07-13
1
3
2021-10-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
The same protein from Dictyostelium discoideum
N
RCSB
Y
RCSB
2004-10-12
REL
REL
TRS
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
PGE
TRIETHYLENE GLYCOL
HOH
water
TRS
200
2
TRS
TRS
200
A
PEG
500
3
PGE
PGE
500
A
TRS
300
2
TRS
TRS
300
B
PEG
600
3
PGE
PGE
600
B
TRS
400
2
TRS
TRS
400
C
PEG
700
3
PGE
PGE
700
C
HOH
6
4
HOH
HOH
501
A
HOH
7
4
HOH
HOH
502
A
HOH
10
4
HOH
HOH
503
A
HOH
17
4
HOH
HOH
504
A
HOH
27
4
HOH
HOH
505
A
HOH
28
4
HOH
HOH
506
A
HOH
30
4
HOH
HOH
507
A
HOH
34
4
HOH
HOH
508
A
HOH
35
4
HOH
HOH
509
A
HOH
37
4
HOH
HOH
510
A
HOH
38
4
HOH
HOH
511
A
HOH
39
4
HOH
HOH
512
A
HOH
40
4
HOH
HOH
513
A
HOH
44
4
HOH
HOH
514
A
HOH
46
4
HOH
HOH
515
A
HOH
48
4
HOH
HOH
516
A
HOH
49
4
HOH
HOH
517
A
HOH
50
4
HOH
HOH
518
A
HOH
53
4
HOH
HOH
519
A
HOH
55
4
HOH
HOH
520
A
HOH
56
4
HOH
HOH
521
A
HOH
64
4
HOH
HOH
522
A
HOH
66
4
HOH
HOH
523
A
HOH
67
4
HOH
HOH
524
A
HOH
69
4
HOH
HOH
525
A
HOH
70
4
HOH
HOH
526
A
HOH
71
4
HOH
HOH
527
A
HOH
72
4
HOH
HOH
528
A
HOH
77
4
HOH
HOH
529
A
HOH
83
4
HOH
HOH
530
A
HOH
93
4
HOH
HOH
531
A
HOH
99
4
HOH
HOH
532
A
HOH
108
4
HOH
HOH
533
A
HOH
109
4
HOH
HOH
534
A
HOH
114
4
HOH
HOH
535
A
HOH
121
4
HOH
HOH
536
A
HOH
122
4
HOH
HOH
537
A
HOH
126
4
HOH
HOH
538
A
HOH
131
4
HOH
HOH
539
A
HOH
134
4
HOH
HOH
540
A
HOH
135
4
HOH
HOH
541
A
HOH
138
4
HOH
HOH
542
A
HOH
144
4
HOH
HOH
543
A
HOH
147
4
HOH
HOH
544
A
HOH
149
4
HOH
HOH
545
A
HOH
157
4
HOH
HOH
546
A
HOH
3
4
HOH
HOH
601
B
HOH
4
4
HOH
HOH
602
B
HOH
12
4
HOH
HOH
603
B
HOH
13
4
HOH
HOH
604
B
HOH
14
4
HOH
HOH
605
B
HOH
15
4
HOH
HOH
606
B
HOH
21
4
HOH
HOH
607
B
HOH
22
4
HOH
HOH
608
B
HOH
23
4
HOH
HOH
609
B
HOH
24
4
HOH
HOH
610
B
HOH
26
4
HOH
HOH
611
B
HOH
31
4
HOH
HOH
612
B
HOH
36
4
HOH
HOH
613
B
HOH
42
4
HOH
HOH
614
B
HOH
45
4
HOH
HOH
615
B
HOH
47
4
HOH
HOH
616
B
HOH
51
4
HOH
HOH
617
B
HOH
52
4
HOH
HOH
618
B
HOH
58
4
HOH
HOH
619
B
HOH
62
4
HOH
HOH
620
B
HOH
73
4
HOH
HOH
621
B
HOH
74
4
HOH
HOH
622
B
HOH
75
4
HOH
HOH
623
B
HOH
76
4
HOH
HOH
624
B
HOH
79
4
HOH
HOH
625
B
HOH
84
4
HOH
HOH
626
B
HOH
86
4
HOH
HOH
627
B
HOH
87
4
HOH
HOH
628
B
HOH
88
4
HOH
HOH
629
B
HOH
89
4
HOH
HOH
630
B
HOH
95
4
HOH
HOH
631
B
HOH
98
4
HOH
HOH
632
B
HOH
100
4
HOH
HOH
633
B
HOH
101
4
HOH
HOH
634
B
HOH
102
4
HOH
HOH
635
B
HOH
103
4
HOH
HOH
636
B
HOH
106
4
HOH
HOH
637
B
HOH
107
4
HOH
HOH
638
B
HOH
110
4
HOH
HOH
639
B
HOH
112
4
HOH
HOH
640
B
HOH
113
4
HOH
HOH
641
B
HOH
115
4
HOH
HOH
642
B
HOH
118
4
HOH
HOH
643
B
HOH
120
4
HOH
HOH
644
B
HOH
123
4
HOH
HOH
645
B
HOH
124
4
HOH
HOH
646
B
HOH
125
4
HOH
HOH
647
B
HOH
129
4
HOH
HOH
648
B
HOH
132
4
HOH
HOH
649
B
HOH
133
4
HOH
HOH
650
B
HOH
139
4
HOH
HOH
651
B
HOH
143
4
HOH
HOH
652
B
HOH
148
4
HOH
HOH
653
B
HOH
152
4
HOH
HOH
654
B
HOH
153
4
HOH
HOH
655
B
HOH
154
4
HOH
HOH
656
B
HOH
155
4
HOH
HOH
657
B
HOH
1
4
HOH
HOH
701
C
HOH
2
4
HOH
HOH
702
C
HOH
5
4
HOH
HOH
703
C
HOH
8
4
HOH
HOH
704
C
HOH
9
4
HOH
HOH
705
C
HOH
11
4
HOH
HOH
706
C
HOH
16
4
HOH
HOH
707
C
HOH
18
4
HOH
HOH
708
C
HOH
19
4
HOH
HOH
709
C
HOH
20
4
HOH
HOH
710
C
HOH
25
4
HOH
HOH
711
C
HOH
29
4
HOH
HOH
712
C
HOH
32
4
HOH
HOH
713
C
HOH
33
4
HOH
HOH
714
C
HOH
41
4
HOH
HOH
715
C
HOH
43
4
HOH
HOH
716
C
HOH
54
4
HOH
HOH
717
C
HOH
57
4
HOH
HOH
718
C
HOH
59
4
HOH
HOH
719
C
HOH
50
4
HOH
HOH
720
C
HOH
61
4
HOH
HOH
721
C
HOH
63
4
HOH
HOH
722
C
HOH
65
4
HOH
HOH
723
C
HOH
68
4
HOH
HOH
724
C
HOH
78
4
HOH
HOH
725
C
HOH
80
4
HOH
HOH
726
C
HOH
81
4
HOH
HOH
727
C
HOH
82
4
HOH
HOH
728
C
HOH
85
4
HOH
HOH
729
C
HOH
90
4
HOH
HOH
730
C
HOH
91
4
HOH
HOH
731
C
HOH
92
4
HOH
HOH
732
C
HOH
94
4
HOH
HOH
733
C
HOH
96
4
HOH
HOH
734
C
HOH
97
4
HOH
HOH
735
C
HOH
104
4
HOH
HOH
736
C
HOH
105
4
HOH
HOH
737
C
HOH
111
4
HOH
HOH
738
C
HOH
116
4
HOH
HOH
739
C
HOH
117
4
HOH
HOH
740
C
HOH
119
4
HOH
HOH
741
C
HOH
127
4
HOH
HOH
742
C
HOH
128
4
HOH
HOH
743
C
HOH
130
4
HOH
HOH
744
C
HOH
136
4
HOH
HOH
745
C
HOH
137
4
HOH
HOH
746
C
HOH
140
4
HOH
HOH
747
C
HOH
141
4
HOH
HOH
748
C
HOH
142
4
HOH
HOH
749
C
HOH
145
4
HOH
HOH
750
C
HOH
146
4
HOH
HOH
751
C
HOH
150
4
HOH
HOH
752
C
HOH
151
4
HOH
HOH
753
C
HOH
156
4
HOH
HOH
754
C
HOH
158
4
HOH
HOH
755
C
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
6
A
n
7
7
A
n
8
8
A
n
9
9
A
n
10
10
A
n
11
11
A
n
12
12
A
n
13
13
A
PRO
14
n
14
PRO
14
A
VAL
15
n
15
VAL
15
A
GLU
16
n
16
GLU
16
A
LYS
17
n
17
LYS
17
A
THR
18
n
18
THR
18
A
LEU
19
n
19
LEU
19
A
LEU
20
n
20
LEU
20
A
ILE
21
n
21
ILE
21
A
LEU
22
n
22
LEU
22
A
LYS
23
n
23
LYS
23
A
PRO
24
n
24
PRO
24
A
ASP
25
n
25
ASP
25
A
ALA
26
n
26
ALA
26
A
VAL
27
n
27
VAL
27
A
ALA
28
n
28
ALA
28
A
ARG
29
n
29
ARG
29
A
GLY
30
n
30
GLY
30
A
LEU
31
n
31
LEU
31
A
VAL
32
n
32
VAL
32
A
ASP
33
n
33
ASP
33
A
GLU
34
n
34
GLU
34
A
ILE
35
n
35
ILE
35
A
ILE
36
n
36
ILE
36
A
SER
37
n
37
SER
37
A
ARG
38
n
38
ARG
38
A
PHE
39
n
39
PHE
39
A
LYS
40
n
40
LYS
40
A
LYS
41
n
41
LYS
41
A
ALA
42
n
42
ALA
42
A
GLY
43
n
43
GLY
43
A
LEU
44
n
44
LEU
44
A
ALA
45
n
45
LYS
45
A
ILE
46
n
46
ILE
46
A
VAL
47
n
47
VAL
47
A
ALA
48
n
48
ALA
48
A
LEU
49
n
49
LEU
49
A
LYS
50
n
50
LYS
50
A
MSE
51
n
51
MSE
51
A
VAL
52
n
52
VAL
52
A
LYS
53
n
53
LYS
53
A
ALA
54
n
54
ALA
54
A
SER
55
n
55
SER
55
A
PRO
56
n
56
PRO
56
A
GLU
57
n
57
GLU
57
A
GLU
58
n
58
GLU
58
A
ILE
59
n
59
ILE
59
A
GLU
60
n
60
GLU
60
A
ARG
61
n
61
ARG
61
A
PHE
62
n
62
PHE
62
A
TYR
63
n
63
TYR
63
A
PRO
64
n
64
PRO
64
A
SER
65
n
65
SER
65
A
SER
66
n
66
SER
66
A
GLU
67
n
67
GLU
67
A
GLU
68
n
68
GLU
68
A
TRP
69
n
69
TRP
69
A
LEU
70
n
70
LEU
70
A
GLN
71
n
71
GLN
71
A
SER
72
n
72
SER
72
A
ALA
73
n
73
ALA
73
A
GLY
74
n
74
GLY
74
A
GLN
75
n
75
GLN
75
A
LYS
76
n
76
LYS
76
A
LEU
77
n
77
LEU
77
A
LEU
78
n
78
LEU
78
A
ALA
79
n
79
LYS
79
A
ALA
80
n
80
ALA
80
A
TYR
81
n
81
TYR
81
A
GLN
82
n
82
GLN
82
A
GLU
83
n
83
GLU
83
A
LEU
84
n
84
LEU
84
A
GLY
85
n
85
GLY
85
A
ILE
86
n
86
ILE
86
A
ASP
87
n
87
ASP
87
A
PRO
88
n
88
PRO
88
A
ARG
89
n
89
ARG
89
A
ALA
90
n
90
ALA
90
A
LYS
91
n
91
LYS
91
A
ILE
92
n
92
ILE
92
A
GLY
93
n
93
GLY
93
A
THR
94
n
94
THR
94
A
ASP
95
n
95
ASP
95
A
ASP
96
n
96
ASP
96
A
PRO
97
n
97
PRO
97
A
VAL
98
n
98
VAL
98
A
GLU
99
n
99
GLU
99
A
VAL
100
n
100
VAL
100
A
GLY
101
n
101
GLY
101
A
ARG
102
n
102
ARG
102
A
ILE
103
n
103
ILE
103
A
ILE
104
n
104
ILE
104
A
LYS
105
n
105
LYS
105
A
ARG
106
n
106
ARG
106
A
ASN
107
n
107
ASN
107
A
LEU
108
n
108
LEU
108
A
VAL
109
n
109
VAL
109
A
LYS
110
n
110
LYS
110
A
TYR
111
n
111
TYR
111
A
MSE
112
n
112
MSE
112
A
THR
113
n
113
THR
113
A
SER
114
n
114
SER
114
A
GLY
115
n
115
GLY
115
A
PRO
116
n
116
PRO
116
A
ASN
117
n
117
ASN
117
A
VAL
118
n
118
VAL
118
A
VAL
119
n
119
VAL
119
A
MSE
120
n
120
MSE
120
A
VAL
121
n
121
VAL
121
A
LEU
122
n
122
LEU
122
A
LYS
123
n
123
LYS
123
A
GLY
124
n
124
GLY
124
A
ASN
125
n
125
ASN
125
A
ARG
126
n
126
ARG
126
A
ALA
127
n
127
ALA
127
A
VAL
128
n
128
VAL
128
A
GLU
129
n
129
GLU
129
A
ILE
130
n
130
ILE
130
A
VAL
131
n
131
VAL
131
A
ARG
132
n
132
ARG
132
A
LYS
133
n
133
LYS
133
A
LEU
134
n
134
LEU
134
A
VAL
135
n
135
VAL
135
A
GLY
136
n
136
GLY
136
A
PRO
137
n
137
PRO
137
A
THR
138
n
138
THR
138
A
SER
139
n
139
SER
139
A
PRO
140
n
140
PRO
140
A
HIS
141
n
141
HIS
141
A
SER
142
n
142
SER
142
A
ALA
143
n
143
ALA
143
A
PRO
144
n
144
PRO
144
A
PRO
145
n
145
PRO
145
A
GLY
146
n
146
GLY
146
A
THR
147
n
147
THR
147
A
ILE
148
n
148
ILE
148
A
ARG
149
n
149
ARG
149
A
GLY
150
n
150
GLY
150
A
ASP
151
n
151
ASP
151
A
TYR
152
n
152
TYR
152
A
SER
153
n
153
SER
153
A
ILE
154
n
154
ILE
154
A
ASP
155
n
155
ASP
155
A
SER
156
n
156
SER
156
A
PRO
157
n
157
PRO
157
A
ASP
158
n
158
ASP
158
A
LEU
159
n
159
LEU
159
A
ALA
160
n
160
ALA
160
A
ALA
161
n
161
ALA
161
A
GLU
162
n
162
GLU
162
A
GLU
163
n
163
GLU
163
A
GLY
164
n
164
GLY
164
A
ARG
165
n
165
ARG
165
A
VAL
166
n
166
VAL
166
A
VAL
167
n
167
VAL
167
A
PHE
168
n
168
PHE
168
A
ASN
169
n
169
ASN
169
A
LEU
170
n
170
LEU
170
A
VAL
171
n
171
VAL
171
A
HIS
172
n
172
HIS
172
A
ALA
173
n
173
ALA
173
A
SER
174
n
174
SER
174
A
ASP
175
n
175
ASP
175
A
SER
176
n
176
SER
176
A
PRO
177
n
177
PRO
177
A
SER
178
n
178
SER
178
A
GLU
179
n
179
GLU
179
A
ALA
180
n
180
ALA
180
A
ALA
181
n
181
GLU
181
A
ARG
182
n
182
ARG
182
A
GLU
183
n
183
GLU
183
A
ILE
184
n
184
ILE
184
A
ARG
185
n
185
ARG
185
A
PHE
186
n
186
PHE
186
A
TRP
187
n
187
TRP
187
A
PHE
188
n
188
PHE
188
A
ARG
189
n
189
ARG
189
A
GLU
190
n
190
GLU
190
A
GLU
191
n
191
GLU
191
A
GLU
192
n
192
GLU
192
A
VAL
193
n
193
VAL
193
A
LEU
194
n
194
LEU
194
A
GLU
195
n
195
GLU
195
A
n
1
1
B
n
2
2
B
n
3
3
B
n
4
4
B
n
5
5
B
n
6
6
B
n
7
7
B
n
8
8
B
n
9
9
B
n
10
10
B
n
11
11
B
n
12
12
B
n
13
13
B
PRO
14
n
14
PRO
14
B
VAL
15
n
15
VAL
15
B
GLU
16
n
16
GLU
16
B
LYS
17
n
17
LYS
17
B
THR
18
n
18
THR
18
B
LEU
19
n
19
LEU
19
B
LEU
20
n
20
LEU
20
B
ILE
21
n
21
ILE
21
B
LEU
22
n
22
LEU
22
B
LYS
23
n
23
LYS
23
B
PRO
24
n
24
PRO
24
B
ASP
25
n
25
ASP
25
B
ALA
26
n
26
ALA
26
B
VAL
27
n
27
VAL
27
B
ALA
28
n
28
ALA
28
B
ARG
29
n
29
ARG
29
B
GLY
30
n
30
GLY
30
B
LEU
31
n
31
LEU
31
B
VAL
32
n
32
VAL
32
B
ASP
33
n
33
ASP
33
B
GLU
34
n
34
GLU
34
B
ILE
35
n
35
ILE
35
B
ILE
36
n
36
ILE
36
B
SER
37
n
37
SER
37
B
ARG
38
n
38
ARG
38
B
PHE
39
n
39
PHE
39
B
LYS
40
n
40
LYS
40
B
LYS
41
n
41
LYS
41
B
ALA
42
n
42
ALA
42
B
GLY
43
n
43
GLY
43
B
LEU
44
n
44
LEU
44
B
ALA
45
n
45
LYS
45
B
ILE
46
n
46
ILE
46
B
VAL
47
n
47
VAL
47
B
ALA
48
n
48
ALA
48
B
LEU
49
n
49
LEU
49
B
LYS
50
n
50
LYS
50
B
MSE
51
n
51
MSE
51
B
VAL
52
n
52
VAL
52
B
LYS
53
n
53
LYS
53
B
ALA
54
n
54
ALA
54
B
SER
55
n
55
SER
55
B
PRO
56
n
56
PRO
56
B
GLU
57
n
57
GLU
57
B
GLU
58
n
58
GLU
58
B
ILE
59
n
59
ILE
59
B
GLU
60
n
60
GLU
60
B
ARG
61
n
61
ARG
61
B
PHE
62
n
62
PHE
62
B
TYR
63
n
63
TYR
63
B
PRO
64
n
64
PRO
64
B
SER
65
n
65
SER
65
B
SER
66
n
66
SER
66
B
GLU
67
n
67
GLU
67
B
GLU
68
n
68
GLU
68
B
TRP
69
n
69
TRP
69
B
LEU
70
n
70
LEU
70
B
GLN
71
n
71
GLN
71
B
SER
72
n
72
SER
72
B
ALA
73
n
73
ALA
73
B
GLY
74
n
74
GLY
74
B
GLN
75
n
75
GLN
75
B
LYS
76
n
76
LYS
76
B
LEU
77
n
77
LEU
77
B
LEU
78
n
78
LEU
78
B
ALA
79
n
79
LYS
79
B
ALA
80
n
80
ALA
80
B
TYR
81
n
81
TYR
81
B
GLN
82
n
82
GLN
82
B
GLU
83
n
83
GLU
83
B
LEU
84
n
84
LEU
84
B
GLY
85
n
85
GLY
85
B
ILE
86
n
86
ILE
86
B
ASP
87
n
87
ASP
87
B
PRO
88
n
88
PRO
88
B
ARG
89
n
89
ARG
89
B
ALA
90
n
90
ALA
90
B
LYS
91
n
91
LYS
91
B
ILE
92
n
92
ILE
92
B
GLY
93
n
93
GLY
93
B
THR
94
n
94
THR
94
B
ASP
95
n
95
ASP
95
B
ASP
96
n
96
ASP
96
B
PRO
97
n
97
PRO
97
B
VAL
98
n
98
VAL
98
B
GLU
99
n
99
GLU
99
B
VAL
100
n
100
VAL
100
B
GLY
101
n
101
GLY
101
B
ARG
102
n
102
ARG
102
B
ILE
103
n
103
ILE
103
B
ILE
104
n
104
ILE
104
B
LYS
105
n
105
LYS
105
B
ARG
106
n
106
ARG
106
B
ASN
107
n
107
ASN
107
B
LEU
108
n
108
LEU
108
B
VAL
109
n
109
VAL
109
B
LYS
110
n
110
LYS
110
B
TYR
111
n
111
TYR
111
B
MSE
112
n
112
MSE
112
B
THR
113
n
113
THR
113
B
SER
114
n
114
SER
114
B
GLY
115
n
115
GLY
115
B
PRO
116
n
116
PRO
116
B
ASN
117
n
117
ASN
117
B
VAL
118
n
118
VAL
118
B
VAL
119
n
119
VAL
119
B
MSE
120
n
120
MSE
120
B
VAL
121
n
121
VAL
121
B
LEU
122
n
122
LEU
122
B
LYS
123
n
123
LYS
123
B
GLY
124
n
124
GLY
124
B
ASN
125
n
125
ASN
125
B
ARG
126
n
126
ARG
126
B
ALA
127
n
127
ALA
127
B
VAL
128
n
128
VAL
128
B
GLU
129
n
129
GLU
129
B
ILE
130
n
130
ILE
130
B
VAL
131
n
131
VAL
131
B
ARG
132
n
132
ARG
132
B
LYS
133
n
133
LYS
133
B
LEU
134
n
134
LEU
134
B
VAL
135
n
135
VAL
135
B
GLY
136
n
136
GLY
136
B
PRO
137
n
137
PRO
137
B
THR
138
n
138
THR
138
B
SER
139
n
139
SER
139
B
PRO
140
n
140
PRO
140
B
HIS
141
n
141
HIS
141
B
SER
142
n
142
SER
142
B
ALA
143
n
143
ALA
143
B
PRO
144
n
144
PRO
144
B
PRO
145
n
145
PRO
145
B
GLY
146
n
146
GLY
146
B
THR
147
n
147
THR
147
B
ILE
148
n
148
ILE
148
B
ARG
149
n
149
ARG
149
B
GLY
150
n
150
GLY
150
B
ASP
151
n
151
ASP
151
B
TYR
152
n
152
TYR
152
B
SER
153
n
153
SER
153
B
ILE
154
n
154
ILE
154
B
ASP
155
n
155
ASP
155
B
SER
156
n
156
SER
156
B
PRO
157
n
157
PRO
157
B
ASP
158
n
158
ASP
158
B
LEU
159
n
159
LEU
159
B
ALA
160
n
160
ALA
160
B
ALA
161
n
161
ALA
161
B
GLU
162
n
162
GLU
162
B
GLU
163
n
163
GLU
163
B
GLY
164
n
164
GLY
164
B
ARG
165
n
165
ARG
165
B
VAL
166
n
166
VAL
166
B
VAL
167
n
167
VAL
167
B
PHE
168
n
168
PHE
168
B
ASN
169
n
169
ASN
169
B
LEU
170
n
170
LEU
170
B
VAL
171
n
171
VAL
171
B
HIS
172
n
172
HIS
172
B
ALA
173
n
173
ALA
173
B
SER
174
n
174
SER
174
B
ASP
175
n
175
ASP
175
B
SER
176
n
176
SER
176
B
PRO
177
n
177
PRO
177
B
SER
178
n
178
SER
178
B
GLU
179
n
179
GLU
179
B
ALA
180
n
180
ALA
180
B
ALA
181
n
181
GLU
181
B
ARG
182
n
182
ARG
182
B
GLU
183
n
183
GLU
183
B
ILE
184
n
184
ILE
184
B
ARG
185
n
185
ARG
185
B
PHE
186
n
186
PHE
186
B
TRP
187
n
187
TRP
187
B
PHE
188
n
188
PHE
188
B
ARG
189
n
189
ARG
189
B
GLU
190
n
190
GLU
190
B
GLU
191
n
191
GLU
191
B
GLU
192
n
192
GLU
192
B
VAL
193
n
193
VAL
193
B
LEU
194
n
194
LEU
194
B
GLU
195
n
195
GLU
195
B
n
1
1
C
n
2
2
C
n
3
3
C
n
4
4
C
n
5
5
C
n
6
6
C
n
7
7
C
n
8
8
C
n
9
9
C
n
10
10
C
n
11
11
C
n
12
12
C
n
13
13
C
PRO
14
n
14
PRO
14
C
VAL
15
n
15
VAL
15
C
GLU
16
n
16
GLU
16
C
LYS
17
n
17
LYS
17
C
THR
18
n
18
THR
18
C
LEU
19
n
19
LEU
19
C
LEU
20
n
20
LEU
20
C
ILE
21
n
21
ILE
21
C
LEU
22
n
22
LEU
22
C
LYS
23
n
23
LYS
23
C
PRO
24
n
24
PRO
24
C
ASP
25
n
25
ASP
25
C
ALA
26
n
26
ALA
26
C
VAL
27
n
27
VAL
27
C
ALA
28
n
28
ALA
28
C
ARG
29
n
29
ARG
29
C
GLY
30
n
30
GLY
30
C
LEU
31
n
31
LEU
31
C
VAL
32
n
32
VAL
32
C
ASP
33
n
33
ASP
33
C
GLU
34
n
34
GLU
34
C
ILE
35
n
35
ILE
35
C
ILE
36
n
36
ILE
36
C
SER
37
n
37
SER
37
C
ARG
38
n
38
ARG
38
C
PHE
39
n
39
PHE
39
C
LYS
40
n
40
LYS
40
C
LYS
41
n
41
LYS
41
C
ALA
42
n
42
ALA
42
C
GLY
43
n
43
GLY
43
C
LEU
44
n
44
LEU
44
C
ALA
45
n
45
LYS
45
C
ILE
46
n
46
ILE
46
C
VAL
47
n
47
VAL
47
C
ALA
48
n
48
ALA
48
C
LEU
49
n
49
LEU
49
C
LYS
50
n
50
LYS
50
C
MSE
51
n
51
MSE
51
C
VAL
52
n
52
VAL
52
C
LYS
53
n
53
LYS
53
C
ALA
54
n
54
ALA
54
C
SER
55
n
55
SER
55
C
PRO
56
n
56
PRO
56
C
GLU
57
n
57
GLU
57
C
GLU
58
n
58
GLU
58
C
ILE
59
n
59
ILE
59
C
GLU
60
n
60
GLU
60
C
ARG
61
n
61
ARG
61
C
PHE
62
n
62
PHE
62
C
TYR
63
n
63
TYR
63
C
PRO
64
n
64
PRO
64
C
SER
65
n
65
SER
65
C
SER
66
n
66
SER
66
C
GLU
67
n
67
GLU
67
C
GLU
68
n
68
GLU
68
C
TRP
69
n
69
TRP
69
C
LEU
70
n
70
LEU
70
C
GLN
71
n
71
GLN
71
C
SER
72
n
72
SER
72
C
ALA
73
n
73
ALA
73
C
GLY
74
n
74
GLY
74
C
GLN
75
n
75
GLN
75
C
LYS
76
n
76
LYS
76
C
LEU
77
n
77
LEU
77
C
LEU
78
n
78
LEU
78
C
ALA
79
n
79
LYS
79
C
ALA
80
n
80
ALA
80
C
TYR
81
n
81
TYR
81
C
GLN
82
n
82
GLN
82
C
GLU
83
n
83
GLU
83
C
LEU
84
n
84
LEU
84
C
GLY
85
n
85
GLY
85
C
ILE
86
n
86
ILE
86
C
ASP
87
n
87
ASP
87
C
PRO
88
n
88
PRO
88
C
ARG
89
n
89
ARG
89
C
ALA
90
n
90
ALA
90
C
LYS
91
n
91
LYS
91
C
ILE
92
n
92
ILE
92
C
GLY
93
n
93
GLY
93
C
THR
94
n
94
THR
94
C
ASP
95
n
95
ASP
95
C
ASP
96
n
96
ASP
96
C
PRO
97
n
97
PRO
97
C
VAL
98
n
98
VAL
98
C
GLU
99
n
99
GLU
99
C
VAL
100
n
100
VAL
100
C
GLY
101
n
101
GLY
101
C
ARG
102
n
102
ARG
102
C
ILE
103
n
103
ILE
103
C
ILE
104
n
104
ILE
104
C
LYS
105
n
105
LYS
105
C
ARG
106
n
106
ARG
106
C
ASN
107
n
107
ASN
107
C
LEU
108
n
108
LEU
108
C
VAL
109
n
109
VAL
109
C
LYS
110
n
110
LYS
110
C
TYR
111
n
111
TYR
111
C
MSE
112
n
112
MSE
112
C
THR
113
n
113
THR
113
C
SER
114
n
114
SER
114
C
GLY
115
n
115
GLY
115
C
PRO
116
n
116
PRO
116
C
ASN
117
n
117
ASN
117
C
VAL
118
n
118
VAL
118
C
VAL
119
n
119
VAL
119
C
MSE
120
n
120
MSE
120
C
VAL
121
n
121
VAL
121
C
LEU
122
n
122
LEU
122
C
LYS
123
n
123
LYS
123
C
GLY
124
n
124
GLY
124
C
ASN
125
n
125
ASN
125
C
ARG
126
n
126
ARG
126
C
ALA
127
n
127
ALA
127
C
VAL
128
n
128
VAL
128
C
GLU
129
n
129
GLU
129
C
ILE
130
n
130
ILE
130
C
VAL
131
n
131
VAL
131
C
ARG
132
n
132
ARG
132
C
LYS
133
n
133
LYS
133
C
LEU
134
n
134
LEU
134
C
VAL
135
n
135
VAL
135
C
GLY
136
n
136
GLY
136
C
PRO
137
n
137
PRO
137
C
THR
138
n
138
THR
138
C
SER
139
n
139
SER
139
C
PRO
140
n
140
PRO
140
C
HIS
141
n
141
HIS
141
C
SER
142
n
142
SER
142
C
ALA
143
n
143
ALA
143
C
PRO
144
n
144
PRO
144
C
PRO
145
n
145
PRO
145
C
GLY
146
n
146
GLY
146
C
THR
147
n
147
THR
147
C
ILE
148
n
148
ILE
148
C
ARG
149
n
149
ARG
149
C
GLY
150
n
150
GLY
150
C
ASP
151
n
151
ASP
151
C
TYR
152
n
152
TYR
152
C
SER
153
n
153
SER
153
C
ILE
154
n
154
ILE
154
C
ASP
155
n
155
ASP
155
C
SER
156
n
156
SER
156
C
PRO
157
n
157
PRO
157
C
ASP
158
n
158
ASP
158
C
LEU
159
n
159
LEU
159
C
ALA
160
n
160
ALA
160
C
ALA
161
n
161
ALA
161
C
GLU
162
n
162
GLU
162
C
GLU
163
n
163
GLU
163
C
GLY
164
n
164
GLY
164
C
ARG
165
n
165
ARG
165
C
VAL
166
n
166
VAL
166
C
VAL
167
n
167
VAL
167
C
PHE
168
n
168
PHE
168
C
ASN
169
n
169
ASN
169
C
LEU
170
n
170
LEU
170
C
VAL
171
n
171
VAL
171
C
HIS
172
n
172
HIS
172
C
ALA
173
n
173
ALA
173
C
SER
174
n
174
SER
174
C
ASP
175
n
175
ASP
175
C
SER
176
n
176
SER
176
C
PRO
177
n
177
PRO
177
C
SER
178
n
178
SER
178
C
GLU
179
n
179
GLU
179
C
ALA
180
n
180
ALA
180
C
ALA
181
n
181
GLU
181
C
ARG
182
n
182
ARG
182
C
GLU
183
n
183
GLU
183
C
ILE
184
n
184
ILE
184
C
ARG
185
n
185
ARG
185
C
PHE
186
n
186
PHE
186
C
TRP
187
n
187
TRP
187
C
PHE
188
n
188
PHE
188
C
ARG
189
n
189
ARG
189
C
GLU
190
n
190
GLU
190
C
GLU
191
n
191
GLU
191
C
GLU
192
n
192
GLU
192
C
VAL
193
n
193
VAL
193
C
LEU
194
n
194
LEU
194
C
GLU
195
n
195
GLU
195
C
author_and_software_defined_assembly
PISA
2
dimeric
author_defined_assembly
2
dimeric
software_defined_assembly
PISA
6
hexameric
2960
13
17440
15860
26
45180
A
MSE
51
SELENOMETHIONINE
A
MSE
51
MET
A
MSE
112
SELENOMETHIONINE
A
MSE
112
MET
A
MSE
120
SELENOMETHIONINE
A
MSE
120
MET
B
MSE
51
SELENOMETHIONINE
B
MSE
51
MET
B
MSE
112
SELENOMETHIONINE
B
MSE
112
MET
B
MSE
120
SELENOMETHIONINE
B
MSE
120
MET
C
MSE
51
SELENOMETHIONINE
C
MSE
51
MET
C
MSE
112
SELENOMETHIONINE
C
MSE
112
MET
C
MSE
120
SELENOMETHIONINE
C
MSE
120
MET
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_656
-x+1,y,-z+1
crystal symmetry operation
53.0158736711
0.0000000000
76.4110451447
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_556
-x,y,-z+1
crystal symmetry operation
-72.0061263289
0.0000000000
76.4110451447
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_445
x-1/2,y-1/2,z
crystal symmetry operation
-62.5110000000
-36.0205000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_546
-x+1/2,y-1/2,-z+1
crystal symmetry operation
-9.4951263289
-36.0205000000
76.4110451447
A
N
VAL
52
A
N
VAL
52
A
O
ASN
117
A
O
ASN
117
A
O
VAL
118
A
O
VAL
118
A
N
LEU
22
A
N
LEU
22
A
N
ILE
21
A
N
ILE
21
A
O
HIS
172
A
O
HIS
172
B
N
VAL
52
B
N
VAL
52
B
O
ASN
117
B
O
ASN
117
B
O
VAL
118
B
O
VAL
118
B
N
LEU
22
B
N
LEU
22
B
N
ILE
21
B
N
ILE
21
B
O
HIS
172
B
O
HIS
172
C
N
VAL
52
C
N
VAL
52
C
O
ASN
117
C
O
ASN
117
C
O
VAL
118
C
O
VAL
118
C
N
LEU
22
C
N
LEU
22
C
N
ILE
21
C
N
ILE
21
C
O
HIS
172
C
O
HIS
172
1
A
CG
LYS
45
A
CG
LYS
45
1
Y
1
A
CD
LYS
45
A
CD
LYS
45
1
Y
1
A
CE
LYS
45
A
CE
LYS
45
1
Y
1
A
NZ
LYS
45
A
NZ
LYS
45
1
Y
1
A
CG
LYS
79
A
CG
LYS
79
1
Y
1
A
CD
LYS
79
A
CD
LYS
79
1
Y
1
A
CE
LYS
79
A
CE
LYS
79
1
Y
1
A
NZ
LYS
79
A
NZ
LYS
79
1
Y
1
A
CG
GLU
181
A
CG
GLU
181
1
Y
1
A
CD
GLU
181
A
CD
GLU
181
1
Y
1
A
OE1
GLU
181
A
OE1
GLU
181
1
Y
1
A
OE2
GLU
181
A
OE2
GLU
181
1
Y
1
B
CG
LYS
45
B
CG
LYS
45
1
Y
1
B
CD
LYS
45
B
CD
LYS
45
1
Y
1
B
CE
LYS
45
B
CE
LYS
45
1
Y
1
B
NZ
LYS
45
B
NZ
LYS
45
1
Y
1
B
CG
LYS
79
B
CG
LYS
79
1
Y
1
B
CD
LYS
79
B
CD
LYS
79
1
Y
1
B
CE
LYS
79
B
CE
LYS
79
1
Y
1
B
NZ
LYS
79
B
NZ
LYS
79
1
Y
1
B
CG
GLU
181
B
CG
GLU
181
1
Y
1
B
CD
GLU
181
B
CD
GLU
181
1
Y
1
B
OE1
GLU
181
B
OE1
GLU
181
1
Y
1
B
OE2
GLU
181
B
OE2
GLU
181
1
Y
1
C
CG
LYS
45
C
CG
LYS
45
1
Y
1
C
CD
LYS
45
C
CD
LYS
45
1
Y
1
C
CE
LYS
45
C
CE
LYS
45
1
Y
1
C
NZ
LYS
45
C
NZ
LYS
45
1
Y
1
C
CG
LYS
79
C
CG
LYS
79
1
Y
1
C
CD
LYS
79
C
CD
LYS
79
1
Y
1
C
CE
LYS
79
C
CE
LYS
79
1
Y
1
C
NZ
LYS
79
C
NZ
LYS
79
1
Y
1
C
CG
GLU
181
C
CG
GLU
181
1
Y
1
C
CD
GLU
181
C
CD
GLU
181
1
Y
1
C
OE1
GLU
181
C
OE1
GLU
181
1
Y
1
C
OE2
GLU
181
C
OE2
GLU
181
1
Y
1
A
MSE
1
A
MSE
1
1
Y
1
A
HIS
2
A
HIS
2
1
Y
1
A
ALA
3
A
ALA
3
1
Y
1
A
ILE
4
A
ILE
4
1
Y
1
A
ASN
5
A
ASN
5
1
Y
1
A
ILE
6
A
ILE
6
1
Y
1
A
ALA
7
A
ALA
7
1
Y
1
A
PHE
8
A
PHE
8
1
Y
1
A
PHE
9
A
PHE
9
1
Y
1
A
ASP
10
A
ASP
10
1
Y
1
A
LEU
11
A
LEU
11
1
Y
1
A
ILE
12
A
ILE
12
1
Y
1
A
MSE
13
A
MSE
13
1
Y
1
B
MSE
1
B
MSE
1
1
Y
1
B
HIS
2
B
HIS
2
1
Y
1
B
ALA
3
B
ALA
3
1
Y
1
B
ILE
4
B
ILE
4
1
Y
1
B
ASN
5
B
ASN
5
1
Y
1
B
ILE
6
B
ILE
6
1
Y
1
B
ALA
7
B
ALA
7
1
Y
1
B
PHE
8
B
PHE
8
1
Y
1
B
PHE
9
B
PHE
9
1
Y
1
B
ASP
10
B
ASP
10
1
Y
1
B
LEU
11
B
LEU
11
1
Y
1
B
ILE
12
B
ILE
12
1
Y
1
B
MSE
13
B
MSE
13
1
Y
1
C
MSE
1
C
MSE
1
1
Y
1
C
HIS
2
C
HIS
2
1
Y
1
C
ALA
3
C
ALA
3
1
Y
1
C
ILE
4
C
ILE
4
1
Y
1
C
ASN
5
C
ASN
5
1
Y
1
C
ILE
6
C
ILE
6
1
Y
1
C
ALA
7
C
ALA
7
1
Y
1
C
PHE
8
C
PHE
8
1
Y
1
C
PHE
9
C
PHE
9
1
Y
1
C
ASP
10
C
ASP
10
1
Y
1
C
LEU
11
C
LEU
11
1
Y
1
C
ILE
12
C
ILE
12
1
Y
1
C
MSE
13
C
MSE
13
1
Y
1
A
A
OD2
OH
ASP
TYR
25
111
2.16
1
5.92
0.90
118.30
124.22
A
A
A
CB
CG
OD1
ASP
ASP
ASP
25
25
25
N
1
-3.85
0.50
120.30
116.45
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
38
38
38
N
1
3.75
0.50
120.30
124.05
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
149
149
149
N
1
-3.56
0.50
120.30
116.74
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
149
149
149
N
1
-10.36
1.70
111.00
100.64
B
B
B
CB
CG
CD2
LEU
LEU
LEU
22
22
22
N
1
3.45
0.50
120.30
123.75
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
89
89
89
N
1
-15.74
2.20
98.90
83.16
C
C
C
CG
SE
CE
MSE
MSE
MSE
51
51
51
N
1
3.10
0.50
120.30
123.40
C
C
C
NE
CZ
NH1
ARG
ARG
ARG
149
149
149
N
1
-4.19
0.50
120.30
116.11
C
C
C
NE
CZ
NH2
ARG
ARG
ARG
149
149
149
N
1
3.75
0.50
120.30
124.05
C
C
C
NE
CZ
NH2
ARG
ARG
ARG
185
185
185
N
1
B
B
NH2
OD2
ARG
ASP
89
95
2.12
1_555
2_757
1
A
LEU
170
77.16
-45.82
1
B
LEU
170
77.87
-38.35
1
C
LEU
170
76.78
-42.45
1
C
GLU
191
-95.28
56.27
37.065
-0.64
0.00
-0.82
0.62
0.00
-1.11
0.944
0.886
0.25964
0.18668
0.19201
2.50
25.0
1620
20785
7.2
94.76
9.260
0.208
RANDOM
1
THROUGHOUT
0
MAD
0.594
0.313
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.50
25.0
158
4454
54
0
4242
0.019
0.022
4365
1.886
2.006
5897
6.445
5.000
543
40.963
23.575
179
20.308
15.000
744
24.981
15.000
38
0.115
0.200
669
0.006
0.020
3211
0.242
0.200
2020
0.315
0.200
2949
0.176
0.200
206
0.244
0.200
117
0.214
0.200
26
0.948
1.500
2821
1.596
2.000
4421
2.549
3.000
1733
4.150
4.500
1476
0.306
0.237
2.565
126
1568
20
98.43
2.4
25
1XQI
25584
22330
0
0.105
1
87.3
2.40
2.55
98.8
refinement
REFMAC
5.2.0005
data reduction
MOSFLM
data scaling
CCP4
(SCALA)
phasing
SOLVE
Crystal Structure Analysis of an NDP kinase from Pyrobaculum aerophilum
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
2
N
N
3
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
A
LYS
23
A
LYS
23
HELX_P
A
ARG
29
A
ARG
29
1
1
7
A
LEU
31
A
LEU
31
HELX_P
A
GLY
43
A
GLY
43
1
2
13
A
SER
55
A
SER
55
HELX_P
A
TYR
63
A
TYR
63
1
3
9
A
SER
66
A
SER
66
HELX_P
A
GLY
85
A
GLY
85
1
4
20
A
ASP
87
A
ASP
87
HELX_P
A
GLY
93
A
GLY
93
1
5
7
A
ASP
96
A
ASP
96
HELX_P
A
THR
113
A
THR
113
1
6
18
A
ARG
126
A
ARG
126
HELX_P
A
GLY
136
A
GLY
136
1
7
11
A
SER
139
A
SER
139
HELX_P
A
ALA
143
A
ALA
143
5
8
5
A
THR
147
A
THR
147
HELX_P
A
SER
153
A
SER
153
1
9
7
A
SER
156
A
SER
156
HELX_P
A
GLU
163
A
GLU
163
1
10
8
A
SER
176
A
SER
176
HELX_P
A
PHE
188
A
PHE
188
1
11
13
A
ARG
189
A
ARG
189
HELX_P
A
VAL
193
A
VAL
193
5
12
5
B
LYS
23
B
LYS
23
HELX_P
B
ARG
29
B
ARG
29
1
13
7
B
LEU
31
B
LEU
31
HELX_P
B
ALA
42
B
ALA
42
1
14
12
B
SER
55
B
SER
55
HELX_P
B
TYR
63
B
TYR
63
1
15
9
B
SER
66
B
SER
66
HELX_P
B
GLY
85
B
GLY
85
1
16
20
B
ASP
87
B
ASP
87
HELX_P
B
ILE
92
B
ILE
92
1
17
6
B
ASP
96
B
ASP
96
HELX_P
B
THR
113
B
THR
113
1
18
18
B
ARG
126
B
ARG
126
HELX_P
B
GLY
136
B
GLY
136
1
19
11
B
SER
139
B
SER
139
HELX_P
B
ALA
143
B
ALA
143
5
20
5
B
THR
147
B
THR
147
HELX_P
B
SER
153
B
SER
153
1
21
7
B
SER
156
B
SER
156
HELX_P
B
GLU
163
B
GLU
163
1
22
8
B
SER
176
B
SER
176
HELX_P
B
PHE
188
B
PHE
188
1
23
13
C
LYS
23
C
LYS
23
HELX_P
C
ARG
29
C
ARG
29
1
24
7
C
LEU
31
C
LEU
31
HELX_P
C
GLY
43
C
GLY
43
1
25
13
C
SER
55
C
SER
55
HELX_P
C
TYR
63
C
TYR
63
1
26
9
C
SER
66
C
SER
66
HELX_P
C
LEU
84
C
LEU
84
1
27
19
C
ASP
87
C
ASP
87
HELX_P
C
ILE
92
C
ILE
92
1
28
6
C
ASP
96
C
ASP
96
HELX_P
C
MSE
112
C
MSE
112
1
29
17
C
ARG
126
C
ARG
126
HELX_P
C
GLY
136
C
GLY
136
1
30
11
C
SER
139
C
SER
139
HELX_P
C
ALA
143
C
ALA
143
5
31
5
C
THR
147
C
THR
147
HELX_P
C
SER
153
C
SER
153
1
32
7
C
SER
156
C
SER
156
HELX_P
C
GLU
163
C
GLU
163
1
33
8
C
SER
176
C
SER
176
HELX_P
C
PHE
188
C
PHE
188
1
34
13
C
ARG
189
C
ARG
189
HELX_P
C
VAL
193
C
VAL
193
5
35
5
covale
1.335
both
A
LYS
50
A
C
LYS
50
1_555
A
MSE
51
A
N
MSE
51
1_555
covale
1.334
both
A
MSE
51
A
C
MSE
51
1_555
A
VAL
52
A
N
VAL
52
1_555
covale
1.339
both
A
TYR
111
A
C
TYR
111
1_555
A
MSE
112
A
N
MSE
112
1_555
covale
1.325
both
A
MSE
112
A
C
MSE
112
1_555
A
THR
113
A
N
THR
113
1_555
covale
1.325
both
A
VAL
119
A
C
VAL
119
1_555
A
MSE
120
A
N
MSE
120
1_555
covale
1.325
both
A
MSE
120
A
C
MSE
120
1_555
A
VAL
121
A
N
VAL
121
1_555
covale
1.330
both
B
LYS
50
B
C
LYS
50
1_555
B
MSE
51
B
N
MSE
51
1_555
covale
1.341
both
B
MSE
51
B
C
MSE
51
1_555
B
VAL
52
B
N
VAL
52
1_555
covale
1.334
both
B
TYR
111
B
C
TYR
111
1_555
B
MSE
112
B
N
MSE
112
1_555
covale
1.326
both
B
MSE
112
B
C
MSE
112
1_555
B
THR
113
B
N
THR
113
1_555
covale
1.333
both
B
VAL
119
B
C
VAL
119
1_555
B
MSE
120
B
N
MSE
120
1_555
covale
1.333
both
B
MSE
120
B
C
MSE
120
1_555
B
VAL
121
B
N
VAL
121
1_555
covale
1.332
both
C
LYS
50
C
C
LYS
50
1_555
C
MSE
51
C
N
MSE
51
1_555
covale
1.339
both
C
MSE
51
C
C
MSE
51
1_555
C
VAL
52
C
N
VAL
52
1_555
covale
1.329
both
C
TYR
111
C
C
TYR
111
1_555
C
MSE
112
C
N
MSE
112
1_555
covale
1.327
both
C
MSE
112
C
C
MSE
112
1_555
C
THR
113
C
N
THR
113
1_555
covale
1.322
both
C
VAL
119
C
C
VAL
119
1_555
C
MSE
120
C
N
MSE
120
1_555
covale
1.321
both
C
MSE
120
C
C
MSE
120
1_555
C
VAL
121
C
N
VAL
121
1_555
TRANSFERASE
alpha/beta sandwich, ferredoxin fold, TRANSFERASE
NDK_PYRAE
UNP
1
1
Q8ZWY4
MHAINIAFFALIMPVEKTLLILKPDAVARGLVGEIISRFEKAGLKIVALKMVKASPEEIERFYPSSEEWLRSAGQKLLKA
YQELGIDPRAKIGTDDPVEVGRIIKRSLVKYMTSGPIVVMVLKGNRAVEIVRKLVGPTSPHSAPPGTIRGDYSIDSPDLA
AEEGRVVFNLVHASDSPSEAEREIRFWFREEEVLE
1
195
1XQI
1
195
Q8ZWY4
A
1
1
195
1
195
1XQI
1
195
Q8ZWY4
B
1
1
195
1
195
1XQI
1
195
Q8ZWY4
C
1
1
195
1
MET
modified residue
MSE
1
1XQI
A
Q8ZWY4
UNP
1
1
1
ALA
engineered mutation
ASP
10
1XQI
A
Q8ZWY4
UNP
10
10
1
MET
modified residue
MSE
13
1XQI
A
Q8ZWY4
UNP
13
13
1
GLY
engineered mutation
ASP
33
1XQI
A
Q8ZWY4
UNP
33
33
1
GLU
engineered mutation
LYS
40
1XQI
A
Q8ZWY4
UNP
40
40
1
MET
modified residue
MSE
51
1XQI
A
Q8ZWY4
UNP
51
51
1
ARG
engineered mutation
GLN
71
1XQI
A
Q8ZWY4
UNP
71
71
1
SER
engineered mutation
ASN
107
1XQI
A
Q8ZWY4
UNP
107
107
1
MET
modified residue
MSE
112
1XQI
A
Q8ZWY4
UNP
112
112
1
ILE
engineered mutation
ASN
117
1XQI
A
Q8ZWY4
UNP
117
117
1
MET
modified residue
MSE
120
1XQI
A
Q8ZWY4
UNP
120
120
2
MET
modified residue
MSE
1
1XQI
B
Q8ZWY4
UNP
1
1
2
ALA
engineered mutation
ASP
10
1XQI
B
Q8ZWY4
UNP
10
10
2
MET
modified residue
MSE
13
1XQI
B
Q8ZWY4
UNP
13
13
2
GLY
engineered mutation
ASP
33
1XQI
B
Q8ZWY4
UNP
33
33
2
GLU
engineered mutation
LYS
40
1XQI
B
Q8ZWY4
UNP
40
40
2
MET
modified residue
MSE
51
1XQI
B
Q8ZWY4
UNP
51
51
2
ARG
engineered mutation
GLN
71
1XQI
B
Q8ZWY4
UNP
71
71
2
SER
engineered mutation
ASN
107
1XQI
B
Q8ZWY4
UNP
107
107
2
MET
modified residue
MSE
112
1XQI
B
Q8ZWY4
UNP
112
112
2
ILE
engineered mutation
ASN
117
1XQI
B
Q8ZWY4
UNP
117
117
2
MET
modified residue
MSE
120
1XQI
B
Q8ZWY4
UNP
120
120
3
MET
modified residue
MSE
1
1XQI
C
Q8ZWY4
UNP
1
1
3
ALA
engineered mutation
ASP
10
1XQI
C
Q8ZWY4
UNP
10
10
3
MET
modified residue
MSE
13
1XQI
C
Q8ZWY4
UNP
13
13
3
GLY
engineered mutation
ASP
33
1XQI
C
Q8ZWY4
UNP
33
33
3
GLU
engineered mutation
LYS
40
1XQI
C
Q8ZWY4
UNP
40
40
3
MET
modified residue
MSE
51
1XQI
C
Q8ZWY4
UNP
51
51
3
ARG
engineered mutation
GLN
71
1XQI
C
Q8ZWY4
UNP
71
71
3
SER
engineered mutation
ASN
107
1XQI
C
Q8ZWY4
UNP
107
107
3
MET
modified residue
MSE
112
1XQI
C
Q8ZWY4
UNP
112
112
3
ILE
engineered mutation
ASN
117
1XQI
C
Q8ZWY4
UNP
117
117
3
MET
modified residue
MSE
120
1XQI
C
Q8ZWY4
UNP
120
120
4
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
45
A
LYS
45
A
VAL
52
A
VAL
52
A
ASN
117
A
ASN
117
A
LYS
123
A
LYS
123
A
LYS
17
A
LYS
17
A
LEU
22
A
LEU
22
A
VAL
171
A
VAL
171
A
ALA
173
A
ALA
173
B
LYS
45
B
LYS
45
B
VAL
52
B
VAL
52
B
ASN
117
B
ASN
117
B
LYS
123
B
LYS
123
B
LYS
17
B
LYS
17
B
LEU
22
B
LEU
22
B
VAL
171
B
VAL
171
B
ALA
173
B
ALA
173
C
LYS
45
C
LYS
45
C
VAL
52
C
VAL
52
C
ASN
117
C
ASN
117
C
LYS
123
C
LYS
123
C
LYS
17
C
LYS
17
C
LEU
22
C
LEU
22
C
VAL
171
C
VAL
171
C
ALA
173
C
ALA
173
BINDING SITE FOR RESIDUE TRS A 200
A
TRS
200
Software
5
BINDING SITE FOR RESIDUE TRS B 300
B
TRS
300
Software
8
BINDING SITE FOR RESIDUE TRS C 400
C
TRS
400
Software
8
BINDING SITE FOR RESIDUE PGE A 500
A
PGE
500
Software
11
BINDING SITE FOR RESIDUE PGE B 600
B
PGE
600
Software
11
BINDING SITE FOR RESIDUE PGE C 700
C
PGE
700
Software
11
A
LYS
23
A
LYS
23
5
1_555
A
TYR
63
A
TYR
63
5
1_555
A
ASN
169
A
ASN
169
5
1_555
A
HIS
172
A
HIS
172
5
1_555
A
PGE
500
E
PGE
5
1_555
B
LYS
23
B
LYS
23
8
1_555
B
TYR
63
B
TYR
63
8
1_555
B
THR
138
B
THR
138
8
1_555
B
ASN
169
B
ASN
169
8
1_555
B
VAL
171
B
VAL
171
8
1_555
B
HIS
172
B
HIS
172
8
1_555
B
PGE
600
G
PGE
8
1_555
B
HOH
613
K
HOH
8
1_555
C
LYS
23
C
LYS
23
8
1_555
C
TYR
63
C
TYR
63
8
1_555
C
THR
138
C
THR
138
8
1_555
C
ASN
169
C
ASN
169
8
1_555
C
HIS
172
C
HIS
172
8
1_555
C
PGE
700
I
PGE
8
1_555
C
HOH
730
L
HOH
8
1_555
C
HOH
755
L
HOH
8
1_555
A
TYR
63
A
TYR
63
11
1_555
A
PRO
64
A
PRO
64
11
1_555
A
TRP
69
A
TRP
69
11
1_555
A
HIS
172
A
HIS
172
11
1_555
A
ALA
173
A
ALA
173
11
1_555
A
SER
174
A
SER
174
11
1_555
A
ASP
175
A
ASP
175
11
1_555
A
GLU
179
A
GLU
179
11
1_555
A
GLU
183
A
GLU
183
11
1_555
A
TRS
200
D
TRS
11
1_555
A
HOH
505
J
HOH
11
1_555
B
TYR
63
B
TYR
63
11
1_555
B
PRO
64
B
PRO
64
11
1_555
B
TRP
69
B
TRP
69
11
1_555
B
HIS
172
B
HIS
172
11
1_555
B
ALA
173
B
ALA
173
11
1_555
B
SER
174
B
SER
174
11
1_555
B
ASP
175
B
ASP
175
11
1_555
B
GLU
179
B
GLU
179
11
1_555
B
GLU
183
B
GLU
183
11
1_555
B
TRS
300
F
TRS
11
1_555
B
HOH
653
K
HOH
11
1_555
C
TYR
63
C
TYR
63
11
1_555
C
PRO
64
C
PRO
64
11
1_555
C
TRP
69
C
TRP
69
11
1_555
C
HIS
172
C
HIS
172
11
1_555
C
ALA
173
C
ALA
173
11
1_555
C
SER
174
C
SER
174
11
1_555
C
ASP
175
C
ASP
175
11
1_555
C
GLU
179
C
GLU
179
11
1_555
C
GLU
183
C
GLU
183
11
1_555
C
TRS
400
H
TRS
11
1_555
C
HOH
749
L
HOH
11
1_555
5
C 1 2 1