0.019105
0.000000
0.000000
-0.000000
0.018599
0.000000
0.000000
-0.000000
0.011799
0.00000
0.00000
0.00000
Chen, S.
Pojer, F.
Heinis, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
52.343
53.766
84.751
C5 H11 N O2 S2
181.276
(4S)-4,5-disulfanyl-L-norvaline
L-peptide linking
C2 H3 O2 -1
59.044
ACETATE ION
non-polymer
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
H2 N
16.023
AMINO GROUP
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
Nat Chem
1755-4349
6
1009
1016
10.1038/nchem.2043
25343607
Dithiol amino acids can structurally shape and enhance the ligand-binding properties of polypeptides.
2014
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
PIXEL
2013-03-18
DECTRIS PILATUS 2M-F
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
1
1.0
X06DA
SLS
1
SYNCHROTRON
SLS BEAMLINE X06DA
27586.420
Urokinase-type plasminogen activator
3.4.21.73
catalytic domain (UNP residues 179-423)
C122A, N145Q
1
man
polymer
1478.791
bicyclic peptide UK602 (bicyclic 1)
1
syn
polymer
96.063
SULFATE ION
2
syn
non-polymer
59.044
ACETATE ION
2
syn
non-polymer
18.015
water
125
nat
water
U-plasminogen activator, uPA, Urokinase-type plasminogen activator long chain A, Urokinase-type plasminogen activator short chain A, Urokinase-type plasminogen activator chain B
no
no
IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVEN
LILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVK
LISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPW
IRSHT
IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVEN
LILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVK
LISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPW
IRSHT
A
polypeptide(L)
no
yes
G(81S)LGRGCENHRCL(NH2)
GXLGRGCENHRCLX
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
human
human
sample
PLAU
9606
Homo sapiens
HEK293
9606
Homo sapiens
plasmid
pSecTagA
1
2.05
40.04
VAPOR DIFFUSION, HANGING DROP
4.5
21% PEG4000, 15% glycerol, 0.17 M ammonium sulfate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
software
entity_src_gen
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Refinement description
Database references
Derived calculations
Source and taxonomy
1
0
2014-09-24
1
1
2014-11-05
1
2
2017-11-22
1
3
2021-06-02
_entity_src_gen.pdbx_host_org_cell_line
_entity_src_gen.pdbx_host_org_strain
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_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_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Human urokinase-type plasminogen activator uPA in complex with the two-disulfide bridge peptide UK504
Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK601 (bicyclic 1)
Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK603 (bicyclic 1)
Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK603 (bicyclic 2)
Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK604 (bicyclic 2)
Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK607 (bicyclic)
RCSB
Y
RCSB
2014-02-12
REL
REL
SO4
SULFATE ION
ACT
ACETATE ION
HOH
water
Inhibitor
bicyclic peptide UK602 (bicyclic 1)
Cyclic peptide
SO4
1
3
SO4
SO4
301
A
SO4
2
3
SO4
SO4
302
A
ACT
1
4
ACT
ACT
303
A
ACT
2
4
ACT
ACT
304
A
HOH
2
5
HOH
HOH
401
A
HOH
3
5
HOH
HOH
402
A
HOH
4
5
HOH
HOH
403
A
HOH
5
5
HOH
HOH
404
A
HOH
6
5
HOH
HOH
405
A
HOH
8
5
HOH
HOH
406
A
HOH
9
5
HOH
HOH
407
A
HOH
10
5
HOH
HOH
408
A
HOH
11
5
HOH
HOH
409
A
HOH
12
5
HOH
HOH
410
A
HOH
13
5
HOH
HOH
411
A
HOH
14
5
HOH
HOH
412
A
HOH
15
5
HOH
HOH
413
A
HOH
17
5
HOH
HOH
414
A
HOH
18
5
HOH
HOH
415
A
HOH
19
5
HOH
HOH
416
A
HOH
20
5
HOH
HOH
417
A
HOH
21
5
HOH
HOH
418
A
HOH
22
5
HOH
HOH
419
A
HOH
23
5
HOH
HOH
420
A
HOH
24
5
HOH
HOH
421
A
HOH
25
5
HOH
HOH
422
A
HOH
26
5
HOH
HOH
423
A
HOH
27
5
HOH
HOH
424
A
HOH
28
5
HOH
HOH
425
A
HOH
29
5
HOH
HOH
426
A
HOH
30
5
HOH
HOH
427
A
HOH
31
5
HOH
HOH
428
A
HOH
32
5
HOH
HOH
429
A
HOH
33
5
HOH
HOH
430
A
HOH
34
5
HOH
HOH
431
A
HOH
35
5
HOH
HOH
432
A
HOH
36
5
HOH
HOH
433
A
HOH
37
5
HOH
HOH
434
A
HOH
38
5
HOH
HOH
435
A
HOH
41
5
HOH
HOH
436
A
HOH
43
5
HOH
HOH
437
A
HOH
44
5
HOH
HOH
438
A
HOH
45
5
HOH
HOH
439
A
HOH
46
5
HOH
HOH
440
A
HOH
47
5
HOH
HOH
441
A
HOH
48
5
HOH
HOH
442
A
HOH
51
5
HOH
HOH
443
A
HOH
53
5
HOH
HOH
444
A
HOH
54
5
HOH
HOH
445
A
HOH
57
5
HOH
HOH
446
A
HOH
58
5
HOH
HOH
447
A
HOH
59
5
HOH
HOH
448
A
HOH
61
5
HOH
HOH
449
A
HOH
62
5
HOH
HOH
450
A
HOH
63
5
HOH
HOH
451
A
HOH
65
5
HOH
HOH
452
A
HOH
66
5
HOH
HOH
453
A
HOH
67
5
HOH
HOH
454
A
HOH
69
5
HOH
HOH
455
A
HOH
71
5
HOH
HOH
456
A
HOH
72
5
HOH
HOH
457
A
HOH
74
5
HOH
HOH
458
A
HOH
75
5
HOH
HOH
459
A
HOH
76
5
HOH
HOH
460
A
HOH
77
5
HOH
HOH
461
A
HOH
79
5
HOH
HOH
462
A
HOH
82
5
HOH
HOH
463
A
HOH
83
5
HOH
HOH
464
A
HOH
84
5
HOH
HOH
465
A
HOH
88
5
HOH
HOH
466
A
HOH
89
5
HOH
HOH
467
A
HOH
91
5
HOH
HOH
468
A
HOH
94
5
HOH
HOH
469
A
HOH
96
5
HOH
HOH
470
A
HOH
97
5
HOH
HOH
471
A
HOH
98
5
HOH
HOH
472
A
HOH
99
5
HOH
HOH
473
A
HOH
100
5
HOH
HOH
474
A
HOH
101
5
HOH
HOH
475
A
HOH
103
5
HOH
HOH
476
A
HOH
105
5
HOH
HOH
477
A
HOH
109
5
HOH
HOH
478
A
HOH
113
5
HOH
HOH
479
A
HOH
114
5
HOH
HOH
480
A
HOH
115
5
HOH
HOH
481
A
HOH
116
5
HOH
HOH
482
A
HOH
120
5
HOH
HOH
483
A
HOH
124
5
HOH
HOH
484
A
HOH
125
5
HOH
HOH
485
A
HOH
130
5
HOH
HOH
486
A
HOH
132
5
HOH
HOH
487
A
HOH
133
5
HOH
HOH
488
A
HOH
135
5
HOH
HOH
489
A
HOH
136
5
HOH
HOH
490
A
HOH
137
5
HOH
HOH
491
A
HOH
138
5
HOH
HOH
492
A
HOH
139
5
HOH
HOH
493
A
HOH
140
5
HOH
HOH
494
A
HOH
141
5
HOH
HOH
495
A
HOH
142
5
HOH
HOH
496
A
HOH
143
5
HOH
HOH
497
A
HOH
144
5
HOH
HOH
498
A
HOH
145
5
HOH
HOH
499
A
HOH
146
5
HOH
HOH
500
A
HOH
147
5
HOH
HOH
501
A
HOH
148
5
HOH
HOH
502
A
HOH
149
5
HOH
HOH
503
A
HOH
150
5
HOH
HOH
504
A
HOH
151
5
HOH
HOH
505
A
HOH
152
5
HOH
HOH
506
A
HOH
153
5
HOH
HOH
507
A
HOH
154
5
HOH
HOH
508
A
HOH
155
5
HOH
HOH
509
A
HOH
156
5
HOH
HOH
510
A
HOH
157
5
HOH
HOH
511
A
HOH
159
5
HOH
HOH
512
A
HOH
160
5
HOH
HOH
513
A
HOH
161
5
HOH
HOH
514
A
HOH
162
5
HOH
HOH
515
A
HOH
163
5
HOH
HOH
516
A
HOH
164
5
HOH
HOH
517
A
HOH
7
5
HOH
HOH
101
B
HOH
39
5
HOH
HOH
102
B
HOH
40
5
HOH
HOH
103
B
HOH
50
5
HOH
HOH
104
B
HOH
52
5
HOH
HOH
105
B
HOH
78
5
HOH
HOH
106
B
HOH
85
5
HOH
HOH
107
B
HOH
90
5
HOH
HOH
108
B
ILE
16
n
1
ILE
16
A
ILE
17
n
2
ILE
17
A
GLY
18
n
3
GLY
18
A
GLY
19
n
4
GLY
19
A
GLU
20
n
5
GLU
20
A
PHE
21
n
6
PHE
21
A
THR
22
n
7
THR
22
A
THR
23
n
8
THR
23
A
ILE
24
n
9
ILE
24
A
GLU
25
n
10
GLU
25
A
ASN
26
n
11
ASN
26
A
GLN
27
n
12
GLN
27
A
PRO
28
n
13
PRO
28
A
TRP
29
n
14
TRP
29
A
PHE
30
n
15
PHE
30
A
ALA
31
n
16
ALA
31
A
ALA
32
n
17
ALA
32
A
ILE
33
n
18
ILE
33
A
TYR
34
n
19
TYR
34
A
ARG
35
n
20
ARG
35
A
ARG
36
n
21
ARG
36
A
HIS
37
n
22
HIS
37
A
ARG
37
n
23
A
ARG
37
A
GLY
37
n
24
B
GLY
37
A
GLY
37
n
25
C
GLY
37
A
SER
37
n
26
D
SER
37
A
VAL
38
n
27
VAL
38
A
THR
39
n
28
THR
39
A
TYR
40
n
29
TYR
40
A
VAL
41
n
30
VAL
41
A
CYS
42
n
31
CYS
42
A
GLY
43
n
32
GLY
43
A
GLY
44
n
33
GLY
44
A
SER
45
n
34
SER
45
A
LEU
46
n
35
LEU
46
A
ILE
47
n
36
ILE
47
A
SER
48
n
37
SER
48
A
PRO
49
n
38
PRO
49
A
CYS
50
n
39
CYS
50
A
TRP
51
n
40
TRP
51
A
VAL
52
n
41
VAL
52
A
ILE
53
n
42
ILE
53
A
SER
54
n
43
SER
54
A
ALA
55
n
44
ALA
55
A
THR
56
n
45
THR
56
A
HIS
57
n
46
HIS
57
A
CYS
58
n
47
CYS
58
A
PHE
59
n
48
PHE
59
A
ILE
60
n
49
ILE
60
A
ASP
60
n
50
A
ASP
60
A
TYR
60
n
51
B
TYR
60
A
PRO
60
n
52
C
PRO
60
A
LYS
61
n
53
LYS
61
A
LYS
62
n
54
LYS
62
A
GLU
62
n
55
A
GLU
62
A
ASP
63
n
56
ASP
63
A
TYR
64
n
57
TYR
64
A
ILE
65
n
58
ILE
65
A
VAL
66
n
59
VAL
66
A
TYR
67
n
60
TYR
67
A
LEU
68
n
61
LEU
68
A
GLY
69
n
62
GLY
69
A
ARG
70
n
63
ARG
70
A
SER
71
n
64
SER
71
A
ARG
72
n
65
ARG
72
A
LEU
73
n
66
LEU
73
A
ASN
74
n
67
ASN
74
A
SER
75
n
68
SER
75
A
ASN
76
n
69
ASN
76
A
THR
77
n
70
THR
77
A
GLN
78
n
71
GLN
78
A
GLY
79
n
72
GLY
79
A
GLU
80
n
73
GLU
80
A
MET
81
n
74
MET
81
A
LYS
82
n
75
LYS
82
A
PHE
83
n
76
PHE
83
A
GLU
84
n
77
GLU
84
A
VAL
85
n
78
VAL
85
A
GLU
86
n
79
GLU
86
A
ASN
87
n
80
ASN
87
A
LEU
88
n
81
LEU
88
A
ILE
89
n
82
ILE
89
A
LEU
90
n
83
LEU
90
A
HIS
91
n
84
HIS
91
A
LYS
92
n
85
LYS
92
A
ASP
93
n
86
ASP
93
A
TYR
94
n
87
TYR
94
A
SER
95
n
88
SER
95
A
ALA
96
n
89
ALA
96
A
ASP
97
n
90
ASP
97
A
THR
97
n
91
A
THR
97
A
LEU
97
n
92
B
LEU
97
A
ALA
98
n
93
ALA
98
A
HIS
99
n
94
HIS
99
A
HIS
100
n
95
HIS
100
A
ASN
101
n
96
ASN
101
A
ASP
102
n
97
ASP
102
A
ILE
103
n
98
ILE
103
A
ALA
104
n
99
ALA
104
A
LEU
105
n
100
LEU
105
A
LEU
106
n
101
LEU
106
A
LYS
107
n
102
LYS
107
A
ILE
108
n
103
ILE
108
A
ARG
109
n
104
ARG
109
A
SER
110
n
105
SER
110
A
LYS
110
n
106
A
LYS
110
A
GLU
110
n
107
B
GLU
110
A
GLY
110
n
108
C
GLY
110
A
ARG
110
n
109
D
ARG
110
A
CYS
111
n
110
CYS
111
A
ALA
112
n
111
ALA
112
A
GLN
113
n
112
GLN
113
A
PRO
114
n
113
PRO
114
A
SER
115
n
114
SER
115
A
ARG
116
n
115
ARG
116
A
THR
117
n
116
THR
117
A
ILE
118
n
117
ILE
118
A
GLN
119
n
118
GLN
119
A
THR
120
n
119
THR
120
A
ILE
121
n
120
ILE
121
A
ALA
122
n
121
ALA
122
A
LEU
123
n
122
LEU
123
A
PRO
124
n
123
PRO
124
A
SER
125
n
124
SER
125
A
MET
126
n
125
MET
126
A
TYR
127
n
126
TYR
127
A
ASN
128
n
127
ASN
128
A
ASP
129
n
128
ASP
129
A
PRO
130
n
129
PRO
130
A
GLN
131
n
130
GLN
131
A
PHE
132
n
131
PHE
132
A
GLY
133
n
132
GLY
133
A
THR
134
n
133
THR
134
A
SER
135
n
134
SER
135
A
CYS
136
n
135
CYS
136
A
GLU
137
n
136
GLU
137
A
ILE
138
n
137
ILE
138
A
THR
139
n
138
THR
139
A
GLY
140
n
139
GLY
140
A
PHE
141
n
140
PHE
141
A
GLY
142
n
141
GLY
142
A
LYS
143
n
142
LYS
143
A
GLU
144
n
143
GLU
144
A
GLN
145
n
144
GLN
145
A
SER
146
n
145
SER
146
A
THR
147
n
146
THR
147
A
ASP
148
n
147
ASP
148
A
TYR
149
n
148
TYR
149
A
LEU
150
n
149
LEU
150
A
TYR
151
n
150
TYR
151
A
PRO
152
n
151
PRO
152
A
GLU
153
n
152
GLU
153
A
GLN
154
n
153
GLN
154
A
LEU
155
n
154
LEU
155
A
LYS
156
n
155
LYS
156
A
MET
157
n
156
MET
157
A
THR
158
n
157
THR
158
A
VAL
159
n
158
VAL
159
A
VAL
160
n
159
VAL
160
A
LYS
161
n
160
LYS
161
A
LEU
162
n
161
LEU
162
A
ILE
163
n
162
ILE
163
A
SER
164
n
163
SER
164
A
HIS
165
n
164
HIS
165
A
ARG
166
n
165
ARG
166
A
GLU
167
n
166
GLU
167
A
CYS
168
n
167
CYS
168
A
GLN
169
n
168
GLN
169
A
GLN
170
n
169
GLN
170
A
PRO
170
n
170
A
PRO
170
A
HIS
170
n
171
B
HIS
170
A
TYR
171
n
172
TYR
171
A
TYR
172
n
173
TYR
172
A
GLY
173
n
174
GLY
173
A
SER
174
n
175
SER
174
A
GLU
175
n
176
GLU
175
A
VAL
176
n
177
VAL
176
A
THR
177
n
178
THR
177
A
THR
178
n
179
THR
178
A
LYS
179
n
180
LYS
179
A
MET
180
n
181
MET
180
A
LEU
181
n
182
LEU
181
A
CYS
182
n
183
CYS
182
A
ALA
183
n
184
ALA
183
A
ALA
184
n
185
ALA
184
A
ASP
185
n
186
ASP
185
A
PRO
185
n
187
A
PRO
185
A
GLN
185
n
188
B
GLN
185
A
TRP
186
n
189
TRP
186
A
LYS
187
n
190
LYS
187
A
THR
188
n
191
THR
188
A
ASP
189
n
192
ASP
189
A
SER
190
n
193
SER
190
A
CYS
191
n
194
CYS
191
A
GLN
192
n
195
GLN
192
A
GLY
193
n
196
GLY
193
A
ASP
194
n
197
ASP
194
A
SER
195
n
198
SER
195
A
GLY
196
n
199
GLY
196
A
GLY
197
n
200
GLY
197
A
PRO
198
n
201
PRO
198
A
LEU
199
n
202
LEU
199
A
VAL
200
n
203
VAL
200
A
CYS
201
n
204
CYS
201
A
SER
202
n
205
SER
202
A
LEU
203
n
206
LEU
203
A
GLN
204
n
207
GLN
204
A
GLY
205
n
208
GLY
205
A
ARG
206
n
209
ARG
206
A
MET
207
n
210
MET
207
A
THR
208
n
211
THR
208
A
LEU
209
n
212
LEU
209
A
THR
210
n
213
THR
210
A
GLY
211
n
214
GLY
211
A
ILE
212
n
215
ILE
212
A
VAL
213
n
216
VAL
213
A
SER
214
n
217
SER
214
A
TRP
215
n
218
TRP
215
A
GLY
216
n
219
GLY
216
A
ARG
217
n
220
ARG
217
A
GLY
218
n
221
GLY
218
A
CYS
220
n
222
CYS
220
A
ALA
221
n
223
ALA
221
A
LEU
222
n
224
LEU
222
A
LYS
223
n
225
LYS
223
A
ASP
223
n
226
A
ASP
223
A
LYS
224
n
227
LYS
224
A
PRO
225
n
228
PRO
225
A
GLY
226
n
229
GLY
226
A
VAL
227
n
230
VAL
227
A
TYR
228
n
231
TYR
228
A
THR
229
n
232
THR
229
A
ARG
230
n
233
ARG
230
A
VAL
231
n
234
VAL
231
A
SER
232
n
235
SER
232
A
HIS
233
n
236
HIS
233
A
PHE
234
n
237
PHE
234
A
LEU
235
n
238
LEU
235
A
PRO
236
n
239
PRO
236
A
TRP
237
n
240
TRP
237
A
ILE
238
n
241
ILE
238
A
ARG
239
n
242
ARG
239
A
SER
240
n
243
SER
240
A
HIS
241
n
244
HIS
241
A
THR
242
n
245
THR
242
A
GLY
1
n
1
GLY
1
B
B1S
2
n
2
81S
2
B
LEU
3
n
3
LEU
3
B
GLY
4
n
4
GLY
4
B
ARG
5
n
5
ARG
5
B
GLY
6
n
6
GLY
6
B
CYS
7
n
7
CYS
7
B
GLU
8
n
8
GLU
8
B
ASN
9
n
9
ASN
9
B
HIS
10
n
10
HIS
10
B
ARG
11
n
11
ARG
11
B
CYS
12
n
12
CYS
12
B
LEU
13
n
13
LEU
13
B
NH2
14
n
14
NH2
14
B
author_and_software_defined_assembly
PISA
2
dimeric
2110
-29
11470
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
GLU
20
A
N
GLU
5
A
O
MET
157
A
O
MET
156
A
N
ILE
163
A
N
ILE
162
A
O
CYS
182
A
O
CYS
183
A
N
LEU
181
A
N
LEU
182
A
O
TYR
228
A
O
TYR
231
A
O
VAL
227
A
O
VAL
230
A
N
TRP
215
A
N
TRP
218
A
O
ARG
206
A
O
ARG
209
A
N
LEU
203
A
N
LEU
206
A
O
VAL
200
A
O
VAL
203
A
N
GLU
137
A
N
GLU
136
A
N
CYS
136
A
N
CYS
135
A
O
VAL
160
A
O
VAL
159
A
N
ILE
33
A
N
ILE
18
A
O
VAL
41
A
O
VAL
30
A
N
SER
45
A
N
SER
34
A
O
ILE
53
A
O
ILE
42
A
N
VAL
52
A
N
VAL
41
A
O
LEU
106
A
O
LEU
101
A
O
LEU
105
A
O
LEU
100
A
N
ILE
89
A
N
ILE
82
A
O
PHE
83
A
O
PHE
76
A
N
VAL
66
A
N
VAL
59
A
O
ILE
65
A
O
ILE
58
A
N
TYR
34
A
N
TYR
19
A
N
SER
95
A
N
SER
88
A
O
HIS
100
A
O
HIS
95
1
A
N
ILE
16
A
N
ILE
1
1
Y
1
A
GLN
27
-140.42
52.87
1
A
VAL
41
-105.07
-64.72
1
A
TYR
171
-89.23
-103.22
1
A
SER
214
-123.33
-57.94
24.760
0.15
-0.00
-0.00
0.17
0.00
-0.32
0.959
0.950
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.20734
0.17953
0.18098
0.18098
1.79
45.40
1152
22952
21724
5.0
99.32
2.726
0.084
RANDOM
1
THROUGHOUT
0
0
MOLECULAR REPLACEMENT
0.135
0.120
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.79
45.40
125
2175
18
0
2032
0.007
0.019
2117
0.003
0.020
1972
1.291
1.956
2871
0.725
3.005
4533
6.002
5.000
260
32.643
23.043
92
15.136
15.000
355
12.848
15.000
15
0.076
0.200
308
0.005
0.021
2381
0.001
0.020
498
0.308
0.283
1.841
80
1452
20
92.34
16.703
1.79
45.4
4OS2
22952
22952
0
0
0.119
1
9.7
8.4
100
0.491
1.79
1.89
3.9
3168
1
7.9
96.3
phasing
PHASES
refinement
REFMAC
5.7.0029
data reduction
XDS
data scaling
SCALA
Urokinase-type plasminogen activator (E.C.3.4.21.73), bicyclic peptide UK602 (bicyclic 1)
Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK602 (bicyclic 1)
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
5
N
N
5
N
N
A
THR
23
A
THR
8
HELX_P
A
GLN
27
A
GLN
12
5
1
5
A
ALA
55
A
ALA
44
HELX_P
A
PHE
59
A
PHE
48
5
2
5
A
LYS
61
A
LYS
53
HELX_P
A
GLU
62
A
GLU
55
5
3
3
A
A
SER
164
A
SER
163
HELX_P
A
GLN
169
A
GLN
168
1
4
6
A
TYR
172
A
TYR
173
HELX_P
A
VAL
176
A
VAL
177
5
5
5
A
PHE
234
A
PHE
237
HELX_P
A
THR
242
A
THR
245
1
6
9
disulf
2.041
A
CYS
42
A
SG
CYS
31
1_555
A
CYS
58
A
SG
CYS
47
1_555
disulf
2.030
A
CYS
50
A
SG
CYS
39
1_555
A
CYS
111
A
SG
CYS
110
1_555
disulf
2.031
A
CYS
136
A
SG
CYS
135
1_555
A
CYS
201
A
SG
CYS
204
1_555
disulf
2.038
A
CYS
168
A
SG
CYS
167
1_555
A
CYS
182
A
SG
CYS
183
1_555
disulf
2.049
A
CYS
191
A
SG
CYS
194
1_555
A
CYS
220
A
SG
CYS
222
1_555
covale
1.331
both
sing
B
GLY
1
B
C
GLY
1
1_555
B
81S
2
B
N
81S
2
1_555
covale
1.338
both
sing
B
81S
2
B
C
81S
2
1_555
B
LEU
3
B
N
LEU
3
1_555
covale
2.041
one
sing
B
81S
2
B
SE
81S
2
1_555
B
CYS
7
B
SG
CYS
7
1_555
covale
2.035
one
sing
B
81S
2
B
SD2
81S
2
1_555
B
CYS
12
B
SG
CYS
12
1_555
covale
1.366
both
sing
B
LEU
13
B
C
LEU
13
1_555
B
NH2
14
B
N
NH2
14
1_555
HYDROLASE/HYDROLASE INHIBITOR
bicyclic peptide, inhibitor, protease, disulfide bridges, cyclization, extracellular, HYDROLASE-HYDROLASE INHIBITOR complex
UROK_HUMAN
UNP
1
179
P00749
IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVEN
LILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICLPSMYNDPQFGTSCEITGFGKENSTDYLYPEQLKMTVVK
LISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPW
IRSHT
4OS2
PDB
2
1
4OS2
G(81S)LGRGCENHRCL(NH2)
179
423
4OS2
16
242
P00749
A
1
1
245
1
14
4OS2
1
14
4OS2
B
2
1
14
1
CYS
engineered mutation
ALA
122
4OS2
A
P00749
UNP
299
121
1
ASN
engineered mutation
GLN
145
4OS2
A
P00749
UNP
322
144
8
7
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLU
20
A
GLU
5
A
PHE
21
A
PHE
6
A
LYS
156
A
LYS
155
A
ILE
163
A
ILE
162
A
MET
180
A
MET
181
A
ALA
184
A
ALA
185
A
GLY
226
A
GLY
229
A
ARG
230
A
ARG
233
A
ARG
206
A
ARG
209
A
TRP
215
A
TRP
218
A
PRO
198
A
PRO
201
A
LEU
203
A
LEU
206
A
SER
135
A
SER
134
A
GLY
140
A
GLY
139
A
LYS
156
A
LYS
155
A
ILE
163
A
ILE
162
A
PHE
30
A
PHE
15
A
ARG
36
A
ARG
21
A
VAL
38
A
VAL
27
A
SER
48
A
SER
37
A
TRP
51
A
TRP
40
A
SER
54
A
SER
43
A
ALA
104
A
ALA
99
A
ARG
109
A
ARG
104
A
MET
81
A
MET
74
A
LEU
90
A
LEU
83
A
TYR
64
A
TYR
57
A
LEU
68
A
LEU
61
A
PHE
30
A
PHE
15
A
ARG
36
A
ARG
21
A
SER
95
A
SER
88
A
ALA
96
A
ALA
89
A
HIS
99
A
HIS
94
A
HIS
100
A
HIS
95
BINDING SITE FOR RESIDUE SO4 A 301
A
SO4
301
Software
6
BINDING SITE FOR RESIDUE SO4 A 302
A
SO4
302
Software
3
BINDING SITE FOR RESIDUE ACT A 303
A
ACT
303
Software
3
BINDING SITE FOR RESIDUE ACT A 304
A
ACT
304
Software
5
BINDING SITE FOR CHAIN B OF BICYCLIC PEPTIDE UK602 (BICYCLIC 1)
Software
34
A
LYS
61
A
LYS
53
6
4_475
A
HIS
100
A
HIS
95
6
1_555
A
THR
177
A
THR
178
6
1_555
A
LYS
179
A
LYS
180
6
1_555
A
MET
180
A
MET
181
6
1_555
A
HOH
511
G
HOH
6
1_555
A
ARG
35
A
ARG
20
3
1_555
A
HIS
37
A
HIS
22
3
1_555
A
ARG
37
A
ARG
23
A
3
1_555
A
THR
23
A
THR
8
3
1_555
A
SER
71
A
SER
64
3
1_555
A
ARG
72
A
ARG
65
3
1_555
A
PHE
132
A
PHE
131
5
1_555
A
SER
164
A
SER
163
5
1_555
A
HIS
165
A
HIS
164
5
1_555
A
ARG
166
A
ARG
165
5
1_555
A
ARG
206
A
ARG
209
5
4_465
A
GLU
20
A
GLU
5
34
3_755
A
PHE
21
A
PHE
6
34
3_755
A
THR
23
A
THR
8
34
3_755
A
ARG
35
A
ARG
20
34
1_555
A
VAL
41
A
VAL
30
34
1_555
A
HIS
57
A
HIS
46
34
1_555
A
CYS
58
A
CYS
47
34
1_555
A
ASP
60
A
ASP
50
A
34
1_555
A
TYR
60
A
TYR
51
B
34
1_555
A
TYR
64
A
TYR
57
34
1_555
A
HIS
99
A
HIS
94
34
1_555
A
GLN
154
A
GLN
153
34
3_755
A
SER
174
A
SER
175
34
4_575
A
ASP
189
A
ASP
192
34
1_555
A
SER
190
A
SER
193
34
1_555
A
CYS
191
A
CYS
194
34
1_555
A
GLN
192
A
GLN
195
34
1_555
A
GLY
193
A
GLY
196
34
1_555
A
SER
195
A
SER
198
34
1_555
A
SER
214
A
SER
217
34
1_555
A
TRP
215
A
TRP
218
34
1_555
A
GLY
218
A
GLY
221
34
1_555
A
GLY
226
A
GLY
229
34
1_555
A
HOH
414
G
HOH
34
1_555
A
HOH
429
G
HOH
34
1_555
A
HOH
449
G
HOH
34
1_555
A
HOH
502
G
HOH
34
3_755
B
HOH
101
H
HOH
34
1_555
B
HOH
102
H
HOH
34
1_555
B
HOH
103
H
HOH
34
1_555
B
HOH
104
H
HOH
34
1_555
B
HOH
105
H
HOH
34
1_555
B
HOH
107
H
HOH
34
1_555
B
HOH
108
H
HOH
34
1_555
19
P 21 21 21