0.022366
0.012913
0.000000
0.000000
0.025826
0.000000
0.000000
0.000000
0.010254
0.00000
0.00000
0.00000
Ratnaparkhi, G.S.
Varadarajan, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
44.710
44.710
97.520
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
C3 H8 N2 O2
104.108
n
AMINOSERINE
L-peptide linking
O4 S -2
96.063
SULFATE ION
non-polymer
C4 H9 N O3
119.119
y
THREONINE
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
39
12365
12374
10.1021/bi000775k
11015216
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics.
2000
US
Proteins: Struct.,Funct.,Genet.
PSFGEY
0867
0887-3585
36
282
294
10.1002/(SICI)1097-0134(19990815)36:3<282::AID-PROT3>3.3.CO;2-6
X-ray crystallographic studies of the denaturation of ribonuclease S
1999
US
Biochemistry
BICHAW
0033
0006-2960
31
12315
12327
Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities
1992
US
Biochemistry
BICHAW
0033
0006-2960
33
8587
8593
Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S
1994
1.000000
.000000
.000000
.000000
1.000000
.000000
.000000
.000000
1.000000
.00000
.00000
.00000
293
1
AREA DETECTOR
1994-03-08
XENTRONICS
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
SYNTHETIC
1675.863
S PEPTIDE
RESIDUES 1-15
F8A
1
syn
polymer
11294.749
RNASE S
RESIDUES 24-124
1
nat
polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
35
nat
water
no
yes
KETAAAKAERQHMD(SET)
KETAAAKAERQHMDS
A
polypeptide(L)
no
no
NYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQAN
KHIIVACEGNPYVPVHFDASV
NYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQAN
KHIIVACEGNPYVPVHFDASV
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
cattle
DERIEVED FROM A LIMIT DIGEST OF BOVINE PANCREATIC RNASE A
Bos
sample
9913
Bos taurus
1
2.17
43.28
VAPOR DIFFUSION, SITTING DROP
5.75
3M CsCl, 35% Ammonium Sulfate. 0.1 M Sodium Acetate, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 20K
293.0
software
exptl_crystal_grow
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Structure summary
Refinement description
Experimental preparation
Database references
1
0
1999-10-20
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-02-01
1
4
2017-10-04
1
5
2018-01-31
1
6
2018-03-14
_exptl_crystal_grow.temp
_struct_ref_seq_dif.details
Control structure for this study, RNase S15.
RELATED STUDY
RELATED STUDY
RCSB
Y
RCSB
1999-10-07
REL
REL
SO4
SULFATE ION
HOH
water
S15 peptide synthesized by solid phase peptide synthesis
sample
SO4
125
3
SO4
SO4
125
B
HOH
202
4
HOH
HOH
202
A
HOH
218
4
HOH
HOH
218
A
HOH
227
4
HOH
HOH
227
A
HOH
236
4
HOH
HOH
236
A
HOH
245
4
HOH
HOH
245
A
HOH
247
4
HOH
HOH
247
A
HOH
201
4
HOH
HOH
201
B
HOH
203
4
HOH
HOH
203
B
HOH
205
4
HOH
HOH
205
B
HOH
207
4
HOH
HOH
207
B
HOH
208
4
HOH
HOH
208
B
HOH
209
4
HOH
HOH
209
B
HOH
210
4
HOH
HOH
210
B
HOH
211
4
HOH
HOH
211
B
HOH
212
4
HOH
HOH
212
B
HOH
213
4
HOH
HOH
213
B
HOH
214
4
HOH
HOH
214
B
HOH
215
4
HOH
HOH
215
B
HOH
216
4
HOH
HOH
216
B
HOH
217
4
HOH
HOH
217
B
HOH
219
4
HOH
HOH
219
B
HOH
221
4
HOH
HOH
221
B
HOH
222
4
HOH
HOH
222
B
HOH
226
4
HOH
HOH
226
B
HOH
228
4
HOH
HOH
228
B
HOH
237
4
HOH
HOH
237
B
HOH
241
4
HOH
HOH
241
B
HOH
243
4
HOH
HOH
243
B
HOH
248
4
HOH
HOH
248
B
HOH
252
4
HOH
HOH
252
B
HOH
255
4
HOH
HOH
255
B
HOH
257
4
HOH
HOH
257
B
HOH
259
4
HOH
HOH
259
B
HOH
260
4
HOH
HOH
260
B
HOH
262
4
HOH
HOH
262
B
LYS
1
n
1
LYS
1
A
GLU
2
n
2
GLU
2
A
THR
3
n
3
THR
3
A
ALA
4
n
4
ALA
4
A
ALA
5
n
5
ALA
5
A
ALA
6
n
6
ALA
6
A
LYS
7
n
7
LYS
7
A
ALA
8
n
8
ALA
8
A
GLU
9
n
9
GLU
9
A
ARG
10
n
10
ARG
10
A
GLN
11
n
11
GLN
11
A
HIS
12
n
12
HIS
12
A
MET
13
n
13
MET
13
A
ASP
14
n
14
ASP
14
A
SET
15
n
15
SET
15
A
ASN
24
n
1
ASN
24
B
TYR
25
n
2
TYR
25
B
CYS
26
n
3
CYS
26
B
ASN
27
n
4
ASN
27
B
GLN
28
n
5
GLN
28
B
MET
29
n
6
MET
29
B
MET
30
n
7
MET
30
B
LYS
31
n
8
LYS
31
B
SER
32
n
9
SER
32
B
ARG
33
n
10
ARG
33
B
ASN
34
n
11
ASN
34
B
LEU
35
n
12
LEU
35
B
THR
36
n
13
THR
36
B
LYS
37
n
14
LYS
37
B
ASP
38
n
15
ASP
38
B
ARG
39
n
16
ARG
39
B
CYS
40
n
17
CYS
40
B
LYS
41
n
18
LYS
41
B
PRO
42
n
19
PRO
42
B
VAL
43
n
20
VAL
43
B
ASN
44
n
21
ASN
44
B
THR
45
n
22
THR
45
B
PHE
46
n
23
PHE
46
B
VAL
47
n
24
VAL
47
B
HIS
48
n
25
HIS
48
B
GLU
49
n
26
GLU
49
B
SER
50
n
27
SER
50
B
LEU
51
n
28
LEU
51
B
ALA
52
n
29
ALA
52
B
ASP
53
n
30
ASP
53
B
VAL
54
n
31
VAL
54
B
GLN
55
n
32
GLN
55
B
ALA
56
n
33
ALA
56
B
VAL
57
n
34
VAL
57
B
CYS
58
n
35
CYS
58
B
SER
59
n
36
SER
59
B
GLN
60
n
37
GLN
60
B
LYS
61
n
38
LYS
61
B
ASN
62
n
39
ASN
62
B
VAL
63
n
40
VAL
63
B
ALA
64
n
41
ALA
64
B
CYS
65
n
42
CYS
65
B
LYS
66
n
43
LYS
66
B
ASN
67
n
44
ASN
67
B
GLY
68
n
45
GLY
68
B
GLN
69
n
46
GLN
69
B
THR
70
n
47
THR
70
B
ASN
71
n
48
ASN
71
B
CYS
72
n
49
CYS
72
B
TYR
73
n
50
TYR
73
B
GLN
74
n
51
GLN
74
B
SER
75
n
52
SER
75
B
TYR
76
n
53
TYR
76
B
SER
77
n
54
SER
77
B
THR
78
n
55
THR
78
B
MET
79
n
56
MET
79
B
SER
80
n
57
SER
80
B
ILE
81
n
58
ILE
81
B
THR
82
n
59
THR
82
B
ASP
83
n
60
ASP
83
B
CYS
84
n
61
CYS
84
B
ARG
85
n
62
ARG
85
B
GLU
86
n
63
GLU
86
B
THR
87
n
64
THR
87
B
GLY
88
n
65
GLY
88
B
SER
89
n
66
SER
89
B
SER
90
n
67
SER
90
B
LYS
91
n
68
LYS
91
B
TYR
92
n
69
TYR
92
B
PRO
93
n
70
PRO
93
B
ASN
94
n
71
ASN
94
B
CYS
95
n
72
CYS
95
B
ALA
96
n
73
ALA
96
B
TYR
97
n
74
TYR
97
B
LYS
98
n
75
LYS
98
B
THR
99
n
76
THR
99
B
THR
100
n
77
THR
100
B
GLN
101
n
78
GLN
101
B
ALA
102
n
79
ALA
102
B
ASN
103
n
80
ASN
103
B
LYS
104
n
81
LYS
104
B
HIS
105
n
82
HIS
105
B
ILE
106
n
83
ILE
106
B
ILE
107
n
84
ILE
107
B
VAL
108
n
85
VAL
108
B
ALA
109
n
86
ALA
109
B
CYS
110
n
87
CYS
110
B
GLU
111
n
88
GLU
111
B
GLY
112
n
89
GLY
112
B
ASN
113
n
90
ASN
113
B
PRO
114
n
91
PRO
114
B
TYR
115
n
92
TYR
115
B
VAL
116
n
93
VAL
116
B
PRO
117
n
94
PRO
117
B
VAL
118
n
95
VAL
118
B
HIS
119
n
96
HIS
119
B
PHE
120
n
97
PHE
120
B
ASP
121
n
98
ASP
121
B
ALA
122
n
99
ALA
122
B
SER
123
n
100
SER
123
B
VAL
124
n
101
VAL
124
B
author_and_software_defined_assembly
PISA
2
dimeric
1730
-22
6460
A
SET
15
AMINOSERINE
A
SET
15
SER
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
B
N
PHE
46
B
N
PHE
23
B
O
THR
82
B
O
THR
59
B
O
ARG
85
B
O
ARG
62
B
N
LYS
98
B
N
LYS
75
B
N
VAL
63
B
N
VAL
40
B
O
CYS
72
B
O
CYS
49
B
N
TYR
73
B
N
TYR
50
B
O
VAL
108
B
O
VAL
85
B
N
GLU
111
B
N
GLU
88
B
O
VAL
116
B
O
VAL
93
1
B
B
HE22
H1
GLN
HOH
60
216
1.30
1
B
TYR
92
-16.74
1
B
B
TYR
PRO
92
93
-95.37
1
9.82
1.40
123.60
133.42
B
B
B
CD
NE
CZ
ARG
ARG
ARG
85
85
85
N
1
9.71
0.50
120.30
130.01
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
85
85
85
N
1
-5.38
0.50
120.30
114.92
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
85
85
85
N
1
16.65
2.00
110.40
127.05
B
B
B
CB
CA
C
TYR
TYR
TYR
92
92
92
N
1
-5.05
0.60
121.00
115.95
B
B
B
CB
CG
CD2
TYR
TYR
TYR
92
92
92
N
1
4.44
0.60
121.00
125.44
B
B
B
CB
CG
CD1
TYR
TYR
TYR
92
92
92
N
1
13.96
1.50
119.30
133.26
B
B
B
C
N
CA
TYR
PRO
PRO
92
93
93
Y
1
-16.10
2.10
128.40
112.30
B
B
B
C
N
CD
TYR
PRO
PRO
92
93
93
Y
1
10.73
1.20
103.30
114.03
B
B
B
N
CA
CB
PRO
PRO
PRO
93
93
93
N
1
B
B
CG
CD1
TYR
TYR
92
92
0.083
0.013
1.387
1.470
N
1
B
B
O
O
HOH
HOH
252
255
0.40
1_555
3_554
1
B
B
H2
O
HOH
HOH
252
255
0.59
1_555
3_554
1
B
B
O
H2
HOH
HOH
252
255
0.69
1_555
3_554
1
B
B
H1
H1
HOH
HOH
252
255
0.89
1_555
3_554
1
A
B
HZ1
H1
LYS
HOH
1
214
0.90
1_555
6_455
1
A
B
HZ1
O
LYS
HOH
1
214
0.96
1_555
6_455
1
B
B
H1
H2
HOH
HOH
252
255
0.96
1_555
3_554
1
B
B
H1
O
HOH
HOH
252
255
1.02
1_555
3_554
1
B
B
O
H1
HOH
HOH
252
255
1.03
1_555
3_554
1
B
B
H2
H1
HOH
HOH
252
255
1.19
1_555
3_554
1
A
B
NZ
O
LYS
HOH
1
214
1.40
1_555
6_455
1
A
B
HZ2
O
LYS
HOH
1
214
1.50
1_555
6_455
1
B
ARG
39
170.77
165.19
1
B
HIS
48
-92.67
50.12
1
B
CYS
58
-64.27
3.20
1
B
GLN
60
-100.20
-131.42
1
B
ASN
67
-65.72
2.21
1
B
TYR
92
-27.95
170.11
1
B
PRO
93
-8.70
-43.30
1
B
ALA
122
177.50
-173.34
1
B
SER
123
-165.49
110.64
PARHCSDX_RV.PRO
TOPHCSDX.PRO
PARAM19.SOL
TOPH.SO4
TOPH19X_WAT.PRO
13.9
.00
.00
.00
.00
.00
.00
NA
0.257
.012
0.21
0.21
0.21
2.25
10.00
557
5238
10.6
92.3
RANDOM
10000000.00
.00
1
RESTRAINED
THROUGHOUT
1.0
NA
.34
.30
3.80
.35
.28
2.25
10.00
35
939
5
0
899
.028
2.8
25.2
6.50
1.82
1.50
2.87
2.00
5.62
2.00
9.64
2.50
0.385
.049
0.305
2.37
62
504
7
11.0
69.8
22.3
2.2
10
1D5H
5328
1
1
0.06
1
13.0
2.5
95
0.3
2.25
2.37
504
1
70
data scaling
X-GEN
data reduction
X-GEN
model building
X-PLOR
refinement
X-PLOR
3.851
phasing
X-PLOR
RNASE S COMPLEXED WITH S PEPTIDE
Rnase s(f8a). mutant ribonucleasE S.
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
Monomer. Two fragments S peptide and S protein held together by non-covalent
interactions
A
THR
3
A
THR
3
HELX_P
A
MET
13
A
MET
13
1
1
11
B
ASN
24
B
ASN
1
HELX_P
B
ARG
33
B
ARG
10
1
2
10
B
SER
50
B
SER
27
HELX_P
B
ALA
56
B
ALA
33
1
3
7
B
VAL
57
B
VAL
34
HELX_P
B
GLN
60
B
GLN
37
5
4
4
disulf
2.032
B
CYS
26
B
SG
CYS
3
1_555
B
CYS
84
B
SG
CYS
61
1_555
disulf
2.008
B
CYS
40
B
SG
CYS
17
1_555
B
CYS
95
B
SG
CYS
72
1_555
disulf
1.788
B
CYS
58
B
SG
CYS
35
1_555
B
CYS
110
B
SG
CYS
87
1_555
disulf
1.994
B
CYS
65
B
SG
CYS
42
1_555
B
CYS
72
B
SG
CYS
49
1_555
covale
1.324
A
ASP
14
A
C
ASP
14
1_555
A
SET
15
A
N
SET
15
1_555
HYDROLASE
RNASE S MUTANT F8A CAVITY S PROTEIN S PEPTIDE, HYDROLASE
B
ASN
113
B
ASN
90
1
B
PRO
114
B
PRO
91
-0.15
RNAS1_BOVIN
UNP
1
P61823
RNP_BOVIN
UNP
2
P00656
1
15
1D5H
1
15
P61823
A
1
1
15
50
150
1D5H
24
124
P00656
B
2
1
101
1
PHE
ENGINEERED MUTATION
ALA
8
1D5H
A
P61823
UNP
8
8
3
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
B
VAL
43
B
VAL
20
B
VAL
47
B
VAL
24
B
MET
79
B
MET
56
B
GLU
86
B
GLU
63
B
TYR
97
B
TYR
74
B
LYS
104
B
LYS
81
B
LYS
61
B
LYS
38
B
VAL
63
B
VAL
40
B
CYS
72
B
CYS
49
B
GLN
74
B
GLN
51
B
ILE
106
B
ILE
83
B
GLU
111
B
GLU
88
B
VAL
116
B
VAL
93
B
SER
123
B
SER
100
BINDING SITE FOR RESIDUE SO4 B 125
Software
4
A
HIS
12
A
HIS
12
4
1_555
B
HIS
119
B
HIS
96
4
1_555
B
PHE
120
B
PHE
97
4
1_555
B
HOH
215
E
HOH
4
1_555
152
P 31 2 1