0.023207
0.000000
0.000000
0.000000
0.009775
0.000000
0.000000
0.000000
0.020125
0.00000
0.00000
0.00000
CIS PROLINE - PRO A 152
Yamamoto, A.
Tomoo, K.
Doi, M.
Ohishi, H.
Inoue, M.
Ishida, T.
Yamamoto, D.
Tsuboi, S.
Okamoto, H.
Okada, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
43.090
102.300
49.690
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
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
C6 H6 N2 O2
138.124
4-NITROANILINE
PARANITROANILINE
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 H6 O4
118.088
SUCCINIC ACID
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
US
Biochemistry
BICHAW
0033
0006-2960
31
11305
11309
10.1021/bi00161a007
1445868
Crystal structure of papain-succinyl-Gln-Val-Val-Ala-Ala-p-nitroanilide complex at 1.7-A resolution: noncovalent binding mode of a common sequence of endogenous thiol protease inhibitors.
1992
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
x-ray
1
1.0
23449.346
PAPAIN
3.4.22.2
1
man
polymer
706.743
SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE
1
syn
polymer
no
no
IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI
HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHA
VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN
IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI
HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHA
VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN
A
polypeptide(L)
no
yes
(SIN)QVVAA(NIT)
XQVVAAX
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
papaya
Carica
sample
3649
Carica papaya
2.27
45.72
pdbx_database_status
struct_conf
struct_conf_type
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Derived calculations
Other
1
0
1993-10-31
1
1
2008-03-24
1
2
2011-07-13
1
3
2012-12-12
1
4
2017-11-29
_pdbx_database_status.process_site
Y
BNL
1992-10-03
REL
SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT
AND PDB SEQUENCE.
SWISS-PROT ENTRY NAME: PAPA_CARPA
SWISS-PROT RESIDUE PDB SEQRES
NAME NUMBER NAME CHAIN SEQ/INSERT CODE
GLU 47 GLN A 47
GLU 118 GLN A 118
GLU 135 GLN A 135
Inhibitor
SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE
Peptide-like
ILE
1
n
1
ILE
1
A
PRO
2
n
2
PRO
2
A
GLU
3
n
3
GLU
3
A
TYR
4
n
4
TYR
4
A
VAL
5
n
5
VAL
5
A
ASP
6
n
6
ASP
6
A
TRP
7
n
7
TRP
7
A
ARG
8
n
8
ARG
8
A
GLN
9
n
9
GLN
9
A
LYS
10
n
10
LYS
10
A
GLY
11
n
11
GLY
11
A
ALA
12
n
12
ALA
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
SER
21
n
21
SER
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
ALA
30
n
30
ALA
30
A
VAL
31
n
31
VAL
31
A
VAL
32
n
32
VAL
32
A
THR
33
n
33
THR
33
A
ILE
34
n
34
ILE
34
A
GLU
35
n
35
GLU
35
A
GLY
36
n
36
GLY
36
A
ILE
37
n
37
ILE
37
A
ILE
38
n
38
ILE
38
A
LYS
39
n
39
LYS
39
A
ILE
40
n
40
ILE
40
A
ARG
41
n
41
ARG
41
A
THR
42
n
42
THR
42
A
GLY
43
n
43
GLY
43
A
ASN
44
n
44
ASN
44
A
LEU
45
n
45
LEU
45
A
ASN
46
n
46
ASN
46
A
GLN
47
n
47
GLN
47
A
TYR
48
n
48
TYR
48
A
SER
49
n
49
SER
49
A
GLU
50
n
50
GLU
50
A
GLN
51
n
51
GLN
51
A
GLU
52
n
52
GLU
52
A
LEU
53
n
53
LEU
53
A
LEU
54
n
54
LEU
54
A
ASP
55
n
55
ASP
55
A
CYS
56
n
56
CYS
56
A
ASP
57
n
57
ASP
57
A
ARG
58
n
58
ARG
58
A
ARG
59
n
59
ARG
59
A
SER
60
n
60
SER
60
A
TYR
61
n
61
TYR
61
A
GLY
62
n
62
GLY
62
A
CYS
63
n
63
CYS
63
A
ASN
64
n
64
ASN
64
A
GLY
65
n
65
GLY
65
A
GLY
66
n
66
GLY
66
A
TYR
67
n
67
TYR
67
A
PRO
68
n
68
PRO
68
A
TRP
69
n
69
TRP
69
A
SER
70
n
70
SER
70
A
ALA
71
n
71
ALA
71
A
LEU
72
n
72
LEU
72
A
GLN
73
n
73
GLN
73
A
LEU
74
n
74
LEU
74
A
VAL
75
n
75
VAL
75
A
ALA
76
n
76
ALA
76
A
GLN
77
n
77
GLN
77
A
TYR
78
n
78
TYR
78
A
GLY
79
n
79
GLY
79
A
ILE
80
n
80
ILE
80
A
HIS
81
n
81
HIS
81
A
TYR
82
n
82
TYR
82
A
ARG
83
n
83
ARG
83
A
ASN
84
n
84
ASN
84
A
THR
85
n
85
THR
85
A
TYR
86
n
86
TYR
86
A
PRO
87
n
87
PRO
87
A
TYR
88
n
88
TYR
88
A
GLU
89
n
89
GLU
89
A
GLY
90
n
90
GLY
90
A
VAL
91
n
91
VAL
91
A
GLN
92
n
92
GLN
92
A
ARG
93
n
93
ARG
93
A
TYR
94
n
94
TYR
94
A
CYS
95
n
95
CYS
95
A
ARG
96
n
96
ARG
96
A
SER
97
n
97
SER
97
A
ARG
98
n
98
ARG
98
A
GLU
99
n
99
GLU
99
A
LYS
100
n
100
LYS
100
A
GLY
101
n
101
GLY
101
A
PRO
102
n
102
PRO
102
A
TYR
103
n
103
TYR
103
A
ALA
104
n
104
ALA
104
A
ALA
105
n
105
ALA
105
A
LYS
106
n
106
LYS
106
A
THR
107
n
107
THR
107
A
ASP
108
n
108
ASP
108
A
GLY
109
n
109
GLY
109
A
VAL
110
n
110
VAL
110
A
ARG
111
n
111
ARG
111
A
GLN
112
n
112
GLN
112
A
VAL
113
n
113
VAL
113
A
GLN
114
n
114
GLN
114
A
PRO
115
n
115
PRO
115
A
TYR
116
n
116
TYR
116
A
ASN
117
n
117
ASN
117
A
GLN
118
n
118
GLN
118
A
GLY
119
n
119
GLY
119
A
ALA
120
n
120
ALA
120
A
LEU
121
n
121
LEU
121
A
LEU
122
n
122
LEU
122
A
TYR
123
n
123
TYR
123
A
SER
124
n
124
SER
124
A
ILE
125
n
125
ILE
125
A
ALA
126
n
126
ALA
126
A
ASN
127
n
127
ASN
127
A
GLN
128
n
128
GLN
128
A
PRO
129
n
129
PRO
129
A
VAL
130
n
130
VAL
130
A
SER
131
n
131
SER
131
A
VAL
132
n
132
VAL
132
A
VAL
133
n
133
VAL
133
A
LEU
134
n
134
LEU
134
A
GLN
135
n
135
GLN
135
A
ALA
136
n
136
ALA
136
A
ALA
137
n
137
ALA
137
A
GLY
138
n
138
GLY
138
A
LYS
139
n
139
LYS
139
A
ASP
140
n
140
ASP
140
A
PHE
141
n
141
PHE
141
A
GLN
142
n
142
GLN
142
A
LEU
143
n
143
LEU
143
A
TYR
144
n
144
TYR
144
A
ARG
145
n
145
ARG
145
A
GLY
146
n
146
GLY
146
A
GLY
147
n
147
GLY
147
A
ILE
148
n
148
ILE
148
A
PHE
149
n
149
PHE
149
A
VAL
150
n
150
VAL
150
A
GLY
151
n
151
GLY
151
A
PRO
152
n
152
PRO
152
A
CYS
153
n
153
CYS
153
A
GLY
154
n
154
GLY
154
A
ASN
155
n
155
ASN
155
A
LYS
156
n
156
LYS
156
A
VAL
157
n
157
VAL
157
A
ASP
158
n
158
ASP
158
A
HIS
159
n
159
HIS
159
A
ALA
160
n
160
ALA
160
A
VAL
161
n
161
VAL
161
A
ALA
162
n
162
ALA
162
A
ALA
163
n
163
ALA
163
A
VAL
164
n
164
VAL
164
A
GLY
165
n
165
GLY
165
A
TYR
166
n
166
TYR
166
A
GLY
167
n
167
GLY
167
A
PRO
168
n
168
PRO
168
A
ASN
169
n
169
ASN
169
A
TYR
170
n
170
TYR
170
A
ILE
171
n
171
ILE
171
A
LEU
172
n
172
LEU
172
A
ILE
173
n
173
ILE
173
A
LYS
174
n
174
LYS
174
A
ASN
175
n
175
ASN
175
A
SER
176
n
176
SER
176
A
TRP
177
n
177
TRP
177
A
GLY
178
n
178
GLY
178
A
THR
179
n
179
THR
179
A
GLY
180
n
180
GLY
180
A
TRP
181
n
181
TRP
181
A
GLY
182
n
182
GLY
182
A
GLU
183
n
183
GLU
183
A
ASN
184
n
184
ASN
184
A
GLY
185
n
185
GLY
185
A
TYR
186
n
186
TYR
186
A
ILE
187
n
187
ILE
187
A
ARG
188
n
188
ARG
188
A
ILE
189
n
189
ILE
189
A
LYS
190
n
190
LYS
190
A
ARG
191
n
191
ARG
191
A
GLY
192
n
192
GLY
192
A
THR
193
n
193
THR
193
A
GLY
194
n
194
GLY
194
A
ASN
195
n
195
ASN
195
A
SER
196
n
196
SER
196
A
TYR
197
n
197
TYR
197
A
GLY
198
n
198
GLY
198
A
VAL
199
n
199
VAL
199
A
CYS
200
n
200
CYS
200
A
GLY
201
n
201
GLY
201
A
LEU
202
n
202
LEU
202
A
TYR
203
n
203
TYR
203
A
THR
204
n
204
THR
204
A
SER
205
n
205
SER
205
A
SER
206
n
206
SER
206
A
PHE
207
n
207
PHE
207
A
TYR
208
n
208
TYR
208
A
PRO
209
n
209
PRO
209
A
VAL
210
n
210
VAL
210
A
LYS
211
n
211
LYS
211
A
ASN
212
n
212
ASN
212
A
SIN
213
n
1
SIN
213
B
GLN
214
n
2
GLN
400
B
VAL
215
n
3
VAL
401
B
VAL
216
n
4
VAL
402
B
ALA
217
n
5
ALA
403
B
ALA
218
n
6
ALA
404
B
NIT
219
n
7
NIT
219
B
author_defined_assembly
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
O
VAL
5
A
O
VAL
5
A
N
TYR
166
A
N
TYR
166
A
O
HIS
159
A
O
HIS
159
A
N
LEU
134
A
N
LEU
134
A
O
SER
131
A
O
SER
131
A
N
PHE
207
A
N
PHE
207
A
O
SER
206
A
O
SER
206
A
N
VAL
113
A
N
VAL
113
A
O
GLY
109
A
O
GLY
109
A
N
LEU
172
A
N
LEU
172
A
O
ILE
171
A
O
ILE
171
A
N
ILE
189
A
N
ILE
189
1
6.05
0.80
106.30
112.35
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
7
7
7
N
1
-5.47
0.80
107.30
101.83
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
7
7
7
N
1
-3.20
0.50
120.30
117.10
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
8
8
8
N
1
4.83
0.80
106.30
111.13
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
26
26
26
N
1
-9.61
1.60
122.70
113.09
A
A
A
O
C
N
CYS
CYS
ASN
63
63
64
Y
1
14.65
2.20
113.40
128.05
A
A
A
CA
CB
CG
ASN
ASN
ASN
64
64
64
N
1
6.66
0.80
106.30
112.96
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
69
69
69
N
1
-5.51
0.80
107.30
101.79
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
69
69
69
N
1
12.65
1.90
113.40
126.05
A
A
A
CA
CB
CG
TYR
TYR
TYR
94
94
94
N
1
4.48
0.50
120.30
124.78
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
98
98
98
N
1
-3.40
0.50
120.30
116.90
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
98
98
98
N
1
-3.73
0.50
120.30
116.57
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
111
111
111
N
1
-4.25
0.60
121.00
116.75
A
A
A
CB
CG
CD2
TYR
TYR
TYR
116
116
116
N
1
-13.37
2.20
111.50
98.13
A
A
A
N
CA
CB
VAL
VAL
VAL
132
132
132
N
1
3.39
0.50
120.30
123.69
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
145
145
145
N
1
10.07
1.60
110.90
120.97
A
A
A
CG1
CB
CG2
VAL
VAL
VAL
161
161
161
N
1
5.28
0.80
106.30
111.58
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
177
177
177
N
1
-4.96
0.80
107.30
102.34
A
A
A
CE2
CD2
CG
TRP
TRP
TRP
177
177
177
N
1
13.61
2.00
116.20
129.81
A
A
A
CA
C
N
TRP
TRP
GLY
177
177
178
Y
1
-11.38
1.70
123.20
111.82
A
A
A
O
C
N
TRP
TRP
GLY
177
177
178
Y
1
5.51
0.80
106.30
111.81
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
181
181
181
N
1
-12.30
1.50
110.90
98.60
B
B
B
CA
CB
CG2
VAL
VAL
VAL
401
401
401
N
1
17.33
2.70
111.00
128.33
B
B
B
N
CA
C
ALA
ALA
ALA
403
403
403
N
1
A
A
NE2
CD2
HIS
HIS
81
81
-0.071
0.011
1.373
1.302
N
1
A
A
NE2
CD2
HIS
HIS
159
159
-0.072
0.011
1.373
1.301
N
1
A
B
CG
C1
GLN
SIN
73
213
2.06
1_555
2_765
1
A
ASN
64
49.93
21.04
1
A
TYR
78
-121.02
-73.69
1
A
TRP
177
-105.00
-160.91
1
B
VAL
401
108.56
126.32
1
B
ALA
403
-33.78
69.26
0.196
0.196
1.7
10.0
1
3.0
1.7
10.0
0
1705
0
0
1705
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
PAPAIN (E.C.3.4.22.2) COMPLEX WITH SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE
CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS
1
N
N
2
N
N
A
SER
24
A
SER
24
HELX_P
INCLUDING 3/10 REGION
A
THR
42
A
THR
42
1
L1
19
A
GLU
50
A
GLU
50
HELX_P
A
ASP
57
A
ASP
57
1
L2
8
A
TYR
67
A
TYR
67
HELX_P
INCLUDING 3/10 REGION
A
TYR
78
A
TYR
78
1
L3
12
A
ASN
117
A
ASN
117
HELX_P
INCLUDING 3/10 REGION
A
ASN
127
A
ASN
127
1
R1
11
A
GLY
138
A
GLY
138
HELX_P
INCLUDING 3/10 REGION
A
GLN
142
A
GLN
142
1
R2
5
disulf
2.021
A
CYS
22
A
SG
CYS
22
1_555
A
CYS
63
A
SG
CYS
63
1_555
disulf
2.044
A
CYS
56
A
SG
CYS
56
1_555
A
CYS
95
A
SG
CYS
95
1_555
disulf
2.023
A
CYS
153
A
SG
CYS
153
1_555
A
CYS
200
A
SG
CYS
200
1_555
covale
1.261
B
SIN
213
B
O2
SIN
1
1_555
A
GLN
73
A
CG
GLN
73
2_764
covale
1.356
B
SIN
213
B
C4
SIN
1
1_555
B
GLN
400
B
N
GLN
2
1_555
covale
1.417
B
ALA
404
B
C
ALA
6
1_555
B
NIT
219
B
N1
NIT
7
1_555
HYDROLASE/HYDROLASE INHIBITOR
THIOL PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
A
GLY
151
A
GLY
151
1
A
PRO
152
A
PRO
152
-2.12
PAPA1_CARPA
UNP
1
134
P00784
1PIP
PDB
2
1PIP
134
345
1PIP
1
212
P00784
A
1
1
212
213
219
1PIP
213
219
1PIP
B
2
1
7
1
GLU
CONFLICT
GLN
47
1PIP
A
P00784
UNP
180
47
1
GLU
CONFLICT
GLN
118
1PIP
A
P00784
UNP
251
118
1
GLU
CONFLICT
GLN
135
1PIP
A
P00784
UNP
268
135
7
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
5
A
VAL
5
A
TRP
7
A
TRP
7
A
ASP
158
A
ASP
158
A
GLY
167
A
GLY
167
A
VAL
130
A
VAL
130
A
LEU
134
A
LEU
134
A
SER
206
A
SER
206
A
VAL
210
A
VAL
210
A
ASP
108
A
ASP
108
A
VAL
113
A
VAL
113
A
TYR
170
A
TYR
170
A
ASN
175
A
ASN
175
A
GLY
185
A
GLY
185
A
ARG
191
A
ARG
191
BINDING SITE FOR CHAIN B OF SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE
Software
8
A
GLN
73
A
GLN
73
8
2_764
A
VAL
110
A
VAL
110
8
2_764
A
ALA
136
A
ALA
136
8
1_555
A
ALA
137
A
ALA
137
8
1_555
A
GLN
142
A
GLN
142
8
1_555
A
LYS
156
A
LYS
156
8
1_555
A
ASP
158
A
ASP
158
8
1_555
A
TRP
177
A
TRP
177
8
1_555
19
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