0.026042
0.000000
0.000000
0.000000
0.019724
0.000000
0.000000
0.000000
0.009533
0.00000
0.00000
0.00000
Zhao, B.
Smith, W.W.
Janson, C.A.
Abdel-Meguid, S.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
38.400
50.700
104.900
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
C15 H30 N5 O5 1
360.429
N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
non-polymer
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
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
4
109
111
10.1038/nsb0297-109
9033588
Crystal structure of human osteoclast cathepsin K complex with E-64.
1997
10.2210/pdb1atk/pdb
pdb_00001atk
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
287
1
MONOCHROMATOR
AREA DETECTOR
1995-10-25
SIEMENS
GRAPHITE(002)
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
SIEMENS
INHIBITOR E-64 COVALENT LINK BETWEEN INHIBITOR ATOM C2 AND THE SULFUR OF CYS 25
23523.480
CATHEPSIN K
3.4.22.38
1
man
polymer
360.429
N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
1
syn
non-polymer
18.015
water
28
nat
water
no
no
APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRG
IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNL
NHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRG
IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNL
NHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
fall armyworm
Spodoptera
sample
HUMAN OSTEOCLASTS
SF21
9606
Homo sapiens
SF21
7108
Spodoptera frugiperda
BACULOVIRUS
1
2.1
43.
VAPOR DIFFUSION
6.2
PROTEIN CRYSTALLIZED FROM 10% PEG 8000, 0.1 M NA/K PHOSPHATE AT PH 6.2 CONTAINING 0.2 M NACL AT ROOM TEMPERATURE BY VAPOR DIFFUSION., vapor diffusion
room temp
diffrn_source
pdbx_database_status
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Other
Database references
Derived calculations
Refinement description
1
0
1998-02-04
1
1
2008-03-24
1
2
2011-07-13
1
3
2018-03-07
1
4
2023-08-02
_diffrn_source.source
_pdbx_database_status.process_site
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_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
1996-12-19
REL
E64
N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
HOH
water
9PAP
PDB ENTRY 9PAP
PDB
experimental model
E64
216
2
E64
E64
216
A
HOH
217
3
HOH
HOH
217
A
HOH
218
3
HOH
HOH
218
A
HOH
219
3
HOH
HOH
219
A
HOH
220
3
HOH
HOH
220
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
223
3
HOH
HOH
223
A
HOH
224
3
HOH
HOH
224
A
HOH
225
3
HOH
HOH
225
A
HOH
226
3
HOH
HOH
226
A
HOH
227
3
HOH
HOH
227
A
HOH
228
3
HOH
HOH
228
A
HOH
229
3
HOH
HOH
229
A
HOH
230
3
HOH
HOH
230
A
HOH
231
3
HOH
HOH
231
A
HOH
232
3
HOH
HOH
232
A
HOH
233
3
HOH
HOH
233
A
HOH
234
3
HOH
HOH
234
A
HOH
235
3
HOH
HOH
235
A
HOH
236
3
HOH
HOH
236
A
HOH
237
3
HOH
HOH
237
A
HOH
238
3
HOH
HOH
238
A
HOH
239
3
HOH
HOH
239
A
HOH
240
3
HOH
HOH
240
A
HOH
241
3
HOH
HOH
241
A
HOH
242
3
HOH
HOH
242
A
HOH
243
3
HOH
HOH
243
A
HOH
244
3
HOH
HOH
244
A
ALA
1
n
1
ALA
1
A
PRO
2
n
2
PRO
2
A
ASP
3
n
3
ASP
3
A
SER
4
n
4
SER
4
A
VAL
5
n
5
VAL
5
A
ASP
6
n
6
ASP
6
A
TYR
7
n
7
TYR
7
A
ARG
8
n
8
ARG
8
A
LYS
9
n
9
LYS
9
A
LYS
10
n
10
LYS
10
A
GLY
11
n
11
GLY
11
A
TYR
12
n
12
TYR
12
A
VAL
13
n
13
VAL
13
A
THR
14
n
14
THR
14
A
PRO
15
n
15
PRO
15
A
VAL
16
n
16
VAL
16
A
LYS
17
n
17
LYS
17
A
ASN
18
n
18
ASN
18
A
GLN
19
n
19
GLN
19
A
GLY
20
n
20
GLY
20
A
GLN
21
n
21
GLN
21
A
CYS
22
n
22
CYS
22
A
GLY
23
n
23
GLY
23
A
SER
24
n
24
SER
24
A
CYS
25
n
25
CYS
25
A
TRP
26
n
26
TRP
26
A
ALA
27
n
27
ALA
27
A
PHE
28
n
28
PHE
28
A
SER
29
n
29
SER
29
A
SER
30
n
30
SER
30
A
VAL
31
n
31
VAL
31
A
GLY
32
n
32
GLY
32
A
ALA
33
n
33
ALA
33
A
LEU
34
n
34
LEU
34
A
GLU
35
n
35
GLU
35
A
GLY
36
n
36
GLY
36
A
GLN
37
n
37
GLN
37
A
LEU
38
n
38
LEU
38
A
LYS
39
n
39
LYS
39
A
LYS
40
n
40
LYS
40
A
LYS
41
n
41
LYS
41
A
THR
42
n
42
THR
42
A
GLY
43
n
43
GLY
43
A
LYS
44
n
44
LYS
44
A
LEU
45
n
45
LEU
45
A
LEU
46
n
46
LEU
46
A
ASN
47
n
47
ASN
47
A
LEU
48
n
48
LEU
48
A
SER
49
n
49
SER
49
A
PRO
50
n
50
PRO
50
A
GLN
51
n
51
GLN
51
A
ASN
52
n
52
ASN
52
A
LEU
53
n
53
LEU
53
A
VAL
54
n
54
VAL
54
A
ASP
55
n
55
ASP
55
A
CYS
56
n
56
CYS
56
A
VAL
57
n
57
VAL
57
A
SER
58
n
58
SER
58
A
GLU
59
n
59
GLU
59
A
ASN
60
n
60
ASN
60
A
ASP
61
n
61
ASP
61
A
GLY
62
n
62
GLY
62
A
CYS
63
n
63
CYS
63
A
GLY
64
n
64
GLY
64
A
GLY
65
n
65
GLY
65
A
GLY
66
n
66
GLY
66
A
TYR
67
n
67
TYR
67
A
MET
68
n
68
MET
68
A
THR
69
n
69
THR
69
A
ASN
70
n
70
ASN
70
A
ALA
71
n
71
ALA
71
A
PHE
72
n
72
PHE
72
A
GLN
73
n
73
GLN
73
A
TYR
74
n
74
TYR
74
A
VAL
75
n
75
VAL
75
A
GLN
76
n
76
GLN
76
A
LYS
77
n
77
LYS
77
A
ASN
78
n
78
ASN
78
A
ARG
79
n
79
ARG
79
A
GLY
80
n
80
GLY
80
A
ILE
81
n
81
ILE
81
A
ASP
82
n
82
ASP
82
A
SER
83
n
83
SER
83
A
GLU
84
n
84
GLU
84
A
ASP
85
n
85
ASP
85
A
ALA
86
n
86
ALA
86
A
TYR
87
n
87
TYR
87
A
PRO
88
n
88
PRO
88
A
TYR
89
n
89
TYR
89
A
VAL
90
n
90
VAL
90
A
GLY
91
n
91
GLY
91
A
GLN
92
n
92
GLN
92
A
GLU
93
n
93
GLU
93
A
GLU
94
n
94
GLU
94
A
SER
95
n
95
SER
95
A
CYS
96
n
96
CYS
96
A
MET
97
n
97
MET
97
A
TYR
98
n
98
TYR
98
A
ASN
99
n
99
ASN
99
A
PRO
100
n
100
PRO
100
A
THR
101
n
101
THR
101
A
GLY
102
n
102
GLY
102
A
LYS
103
n
103
LYS
103
A
ALA
104
n
104
ALA
104
A
ALA
105
n
105
ALA
105
A
LYS
106
n
106
LYS
106
A
CYS
107
n
107
CYS
107
A
ARG
108
n
108
ARG
108
A
GLY
109
n
109
GLY
109
A
TYR
110
n
110
TYR
110
A
ARG
111
n
111
ARG
111
A
GLU
112
n
112
GLU
112
A
ILE
113
n
113
ILE
113
A
PRO
114
n
114
PRO
114
A
GLU
115
n
115
GLU
115
A
GLY
116
n
116
GLY
116
A
ASN
117
n
117
ASN
117
A
GLU
118
n
118
GLU
118
A
LYS
119
n
119
LYS
119
A
ALA
120
n
120
ALA
120
A
LEU
121
n
121
LEU
121
A
LYS
122
n
122
LYS
122
A
ARG
123
n
123
ARG
123
A
ALA
124
n
124
ALA
124
A
VAL
125
n
125
VAL
125
A
ALA
126
n
126
ALA
126
A
ARG
127
n
127
ARG
127
A
VAL
128
n
128
VAL
128
A
GLY
129
n
129
GLY
129
A
PRO
130
n
130
PRO
130
A
VAL
131
n
131
VAL
131
A
SER
132
n
132
SER
132
A
VAL
133
n
133
VAL
133
A
ALA
134
n
134
ALA
134
A
ILE
135
n
135
ILE
135
A
ASP
136
n
136
ASP
136
A
ALA
137
n
137
ALA
137
A
SER
138
n
138
SER
138
A
LEU
139
n
139
LEU
139
A
THR
140
n
140
THR
140
A
SER
141
n
141
SER
141
A
PHE
142
n
142
PHE
142
A
GLN
143
n
143
GLN
143
A
PHE
144
n
144
PHE
144
A
TYR
145
n
145
TYR
145
A
SER
146
n
146
SER
146
A
LYS
147
n
147
LYS
147
A
GLY
148
n
148
GLY
148
A
VAL
149
n
149
VAL
149
A
TYR
150
n
150
TYR
150
A
TYR
151
n
151
TYR
151
A
ASP
152
n
152
ASP
152
A
GLU
153
n
153
GLU
153
A
SER
154
n
154
SER
154
A
CYS
155
n
155
CYS
155
A
ASN
156
n
156
ASN
156
A
SER
157
n
157
SER
157
A
ASP
158
n
158
ASP
158
A
ASN
159
n
159
ASN
159
A
LEU
160
n
160
LEU
160
A
ASN
161
n
161
ASN
161
A
HIS
162
n
162
HIS
162
A
ALA
163
n
163
ALA
163
A
VAL
164
n
164
VAL
164
A
LEU
165
n
165
LEU
165
A
ALA
166
n
166
ALA
166
A
VAL
167
n
167
VAL
167
A
GLY
168
n
168
GLY
168
A
TYR
169
n
169
TYR
169
A
GLY
170
n
170
GLY
170
A
ILE
171
n
171
ILE
171
A
GLN
172
n
172
GLN
172
A
LYS
173
n
173
LYS
173
A
GLY
174
n
174
GLY
174
A
ASN
175
n
175
ASN
175
A
LYS
176
n
176
LYS
176
A
HIS
177
n
177
HIS
177
A
TRP
178
n
178
TRP
178
A
ILE
179
n
179
ILE
179
A
ILE
180
n
180
ILE
180
A
LYS
181
n
181
LYS
181
A
ASN
182
n
182
ASN
182
A
SER
183
n
183
SER
183
A
TRP
184
n
184
TRP
184
A
GLY
185
n
185
GLY
185
A
GLU
186
n
186
GLU
186
A
ASN
187
n
187
ASN
187
A
TRP
188
n
188
TRP
188
A
GLY
189
n
189
GLY
189
A
ASN
190
n
190
ASN
190
A
LYS
191
n
191
LYS
191
A
GLY
192
n
192
GLY
192
A
TYR
193
n
193
TYR
193
A
ILE
194
n
194
ILE
194
A
LEU
195
n
195
LEU
195
A
MET
196
n
196
MET
196
A
ALA
197
n
197
ALA
197
A
ARG
198
n
198
ARG
198
A
ASN
199
n
199
ASN
199
A
LYS
200
n
200
LYS
200
A
ASN
201
n
201
ASN
201
A
ASN
202
n
202
ASN
202
A
ALA
203
n
203
ALA
203
A
CYS
204
n
204
CYS
204
A
GLY
205
n
205
GLY
205
A
ILE
206
n
206
ILE
206
A
ALA
207
n
207
ALA
207
A
ASN
208
n
208
ASN
208
A
LEU
209
n
209
LEU
209
A
ALA
210
n
210
ALA
210
A
SER
211
n
211
SER
211
A
PHE
212
n
212
PHE
212
A
PRO
213
n
213
PRO
213
A
LYS
214
n
214
LYS
214
A
MET
215
n
215
MET
215
A
author_defined_assembly
1
monomeric
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
ARG
111
A
O
ARG
111
A
N
PHE
212
A
N
PHE
212
A
O
VAL
131
A
O
VAL
131
A
N
ALA
166
A
N
ALA
166
A
O
LEU
165
A
O
LEU
165
A
N
LYS
181
A
N
LYS
181
A
O
TRP
178
A
O
TRP
178
A
N
MET
196
A
N
MET
196
1
A
GLN
21
-90.24
46.54
1
A
ARG
79
71.84
38.67
1
A
TYR
87
-157.97
73.51
1
A
ASN
159
-142.31
56.19
1
A
GLN
172
-90.09
-110.70
1
A
LYS
200
-113.30
56.62
PARHCSDX.PRO
TOPHCSDX.PRO
0.31
0.095
0.215
0.215
2.20
7.00
1061
10052
8.7
84.7
RANDOM
100000.
0.1
1
2.
MOLECULAR REPLACEMENT
PDB ENTRY 9PAP
7.0
2.20
7.00
89
1852
26
0
1737
0.007
1.51
22.8
1.1
2.3
8
66.4
2.20
25.
1ATK
10418
2.
0.095
0.095
1
14.
3.2
95.
0.19
2.20
2.34
2.94
0.19
2.3
80.
data collection
XENGEN
data reduction
XENGEN
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
data scaling
XENGEN
phasing
X-PLOR
3.1
CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH THE COVALENT INHIBITOR E-64
1
N
N
2
N
N
3
N
N
A
TYR
7
A
TYR
7
HELX_P
A
LYS
10
A
LYS
10
5
1
4
A
CYS
25
A
CYS
25
HELX_P
A
THR
42
A
THR
42
1
2
18
A
PRO
50
A
PRO
50
HELX_P
A
CYS
56
A
CYS
56
1
3
7
A
GLY
62
A
GLY
62
HELX_P
A
GLY
64
A
GLY
64
5
4
3
A
MET
68
A
MET
68
HELX_P
A
ASN
78
A
ASN
78
1
5
11
A
PRO
100
A
PRO
100
HELX_P
A
GLY
102
A
GLY
102
5
6
3
A
GLU
118
A
GLU
118
HELX_P
A
ARG
127
A
ARG
127
1
7
10
A
THR
140
A
THR
140
HELX_P
A
GLN
143
A
GLN
143
1
8
4
A
ALA
203
A
ALA
203
HELX_P
A
GLY
205
A
GLY
205
5
9
3
disulf
2.035
A
CYS
22
A
SG
CYS
22
1_555
A
CYS
63
A
SG
CYS
63
1_555
disulf
2.028
A
CYS
56
A
SG
CYS
56
1_555
A
CYS
96
A
SG
CYS
96
1_555
disulf
2.033
A
CYS
155
A
SG
CYS
155
1_555
A
CYS
204
A
SG
CYS
204
1_555
covale
1.797
none
A
CYS
25
A
SG
CYS
25
1_555
A
E64
216
B
C2
E64
1_555
HYDROLASE
HYDROLASE, SULFHYDRYL PROTEINASE
CATK_HUMAN
UNP
1
1
P43235
MWGLKVLLLPVVSFALYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMNHLGD
MTSEEVVQKMTGLKVPLSHSRSNDTLYIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLL
NLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVA
RVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGI
ANLASFPKM
115
329
1ATK
1
215
P43235
A
1
1
215
2
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
110
A
TYR
110
A
GLU
112
A
GLU
112
A
SER
211
A
SER
211
A
PRO
213
A
PRO
213
A
VAL
131
A
VAL
131
A
ILE
135
A
ILE
135
A
HIS
162
A
HIS
162
A
ILE
171
A
ILE
171
A
LYS
176
A
LYS
176
A
LYS
181
A
LYS
181
A
TYR
193
A
TYR
193
A
ALA
197
A
ALA
197
BINDING SITE FOR RESIDUE E64 A 216
A
E64
216
Software
17
A
SER
4
A
SER
4
17
1_655
A
GLN
19
A
GLN
19
17
1_555
A
GLY
23
A
GLY
23
17
1_555
A
SER
24
A
SER
24
17
1_555
A
CYS
25
A
CYS
25
17
1_555
A
TRP
26
A
TRP
26
17
1_555
A
GLU
59
A
GLU
59
17
1_555
A
ASN
60
A
ASN
60
17
1_555
A
ASP
61
A
ASP
61
17
1_555
A
GLY
65
A
GLY
65
17
1_555
A
GLY
66
A
GLY
66
17
1_555
A
TYR
67
A
TYR
67
17
1_555
A
LEU
160
A
LEU
160
17
1_555
A
ASN
161
A
ASN
161
17
1_555
A
HIS
162
A
HIS
162
17
1_555
A
HOH
225
C
HOH
17
1_555
A
HOH
232
C
HOH
17
1_555
19
P 21 21 21