.022432
.012951
.000000
.000000
.025902
.000000
.000000
.000000
.010227
.00000
.00000
.00000
Ratnaparkhi, G.S.
Varadarajan, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
44.580
44.580
97.780
C4 H9 N O2
103.120
n
ALPHA-AMINOISOBUTYRIC ACID
L-peptide linking
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
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
UK
Protein Eng.
PRENE9
0859
0269-2139
13
697
702
10.1093/protein/13.10.697
11112508
Structural and thermodynamic consequences of introducing alpha-aminoisobutyric acid in the S peptide of ribonuclease S.
2000
To be Published
0353
Thermodynamic and Structural Studies of Cavity Formation in Proteins Suggest that Loss of Packing Interactions Rather than the Hydrophobic Effect Dominates the Observed Energetics
US
Proteins
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
10.2210/pdb1fev/pdb
pdb_00001fev
1.000000
.000000
.000000
.000000
1.000000
.000000
.000000
.000000
1.000000
.00000
.00000
.00000
298
1
IMAGE PLATE
1996-08-26
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
1748.933
S PEPTIDE
1
syn
polymer
11294.749
S PROTEIN
3.1.27.5
1
nat
polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
42
nat
water
RNASE S
no
yes
KET(AIB)AAKFERQHLDS
KETAAAKFERQHLDS
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
Bos
sample
9913
Bos taurus
PANCREAS
1
2.15
42.78
VAPOR DIFFUSION, SITTING DROP
5.75
3M CsCl, 35% Ammonium Sulphate, 50 mM Sodium Acetate, pH=5.75 , VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
software
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Database references
Derived calculations
1
0
2000-08-09
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2021-11-03
_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
1D5D contains mutant RNase S: F8M
1D5E contains mutant RNase S: F8Nle
1D5H contains mutant RNase S: F8A
1RNV contains wildtype RNase S
1RBH contains mutant RNase S: M13L
RCSB
Y
RCSB
2000-07-23
REL
REL
SO4
SULFATE ION
HOH
water
S peptide is a 16 residue synthetic peptide with Ala4Aib replacement
sample
SO4
125
3
SO4
SO4
125
B
WAT
202
4
HOH
HOH
202
A
WAT
204
4
HOH
HOH
204
A
WAT
218
4
HOH
HOH
218
A
WAT
222
4
HOH
HOH
222
A
WAT
230
4
HOH
HOH
230
A
WAT
236
4
HOH
HOH
236
A
WAT
239
4
HOH
HOH
239
A
WAT
247
4
HOH
HOH
247
A
WAT
259
4
HOH
HOH
259
A
WAT
201
4
HOH
HOH
201
B
WAT
203
4
HOH
HOH
203
B
WAT
205
4
HOH
HOH
205
B
WAT
206
4
HOH
HOH
206
B
WAT
207
4
HOH
HOH
207
B
WAT
208
4
HOH
HOH
208
B
WAT
209
4
HOH
HOH
209
B
WAT
210
4
HOH
HOH
210
B
WAT
211
4
HOH
HOH
211
B
WAT
212
4
HOH
HOH
212
B
WAT
213
4
HOH
HOH
213
B
WAT
214
4
HOH
HOH
214
B
WAT
215
4
HOH
HOH
215
B
WAT
216
4
HOH
HOH
216
B
WAT
217
4
HOH
HOH
217
B
WAT
220
4
HOH
HOH
220
B
WAT
221
4
HOH
HOH
221
B
WAT
225
4
HOH
HOH
225
B
WAT
226
4
HOH
HOH
226
B
WAT
227
4
HOH
HOH
227
B
WAT
228
4
HOH
HOH
228
B
WAT
231
4
HOH
HOH
231
B
WAT
235
4
HOH
HOH
235
B
WAT
237
4
HOH
HOH
237
B
WAT
240
4
HOH
HOH
240
B
WAT
241
4
HOH
HOH
241
B
WAT
243
4
HOH
HOH
243
B
WAT
245
4
HOH
HOH
245
B
WAT
246
4
HOH
HOH
246
B
WAT
252
4
HOH
HOH
252
B
WAT
257
4
HOH
HOH
257
B
WAT
263
4
HOH
HOH
263
B
WAT
265
4
HOH
HOH
265
B
LYS
1
n
1
LYS
1
A
GLU
2
n
2
GLU
2
A
THR
3
n
3
THR
3
A
AIB
4
n
4
AIB
4
A
ALA
5
n
5
ALA
5
A
ALA
6
n
6
ALA
6
A
LYS
7
n
7
LYS
7
A
PHE
8
n
8
PHE
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
LEU
13
n
13
LEU
13
A
ASP
14
n
14
ASP
14
A
SER
15
n
15
SER
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
software_defined_assembly
PISA
4
tetrameric
1620
-23
6540
5210
-52
11110
A
AIB
4
ALPHA-AMINOISOBUTYRIC ACID
A
AIB
4
ALA
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
-0.5000000000
0.8660254038
0.0000000000
0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
B
N
VAL
124
B
N
VAL
101
B
O
HIS
105
B
O
HIS
82
B
O
VAL
108
B
O
VAL
85
B
N
TYR
73
B
N
TYR
50
B
N
GLN
74
B
N
GLN
51
B
O
LYS
61
B
O
LYS
38
B
N
VAL
124
B
N
VAL
101
B
O
HIS
105
B
O
HIS
82
B
O
LYS
104
B
O
LYS
81
B
N
MET
79
B
N
MET
56
B
N
CYS
84
B
N
CYS
61
B
O
ASN
44
B
O
ASN
21
1
B
GLN
60
-98.78
-131.99
1
B
THR
70
-108.54
42.60
1
B
ASN
94
-103.69
61.84
1
B
ALA
122
162.89
178.94
parhcsdx_rv.pro
TOPHCSD.pro
param19.sol
TOPH.SO4
TOPH19X_WAT.PRO
17.5
.00
.00
.00
.00
.00
.00
0.229
.011
0.191
0.191
2.25
10.00
476
4654
10.2
82.3
RANDOM
10000000.00
.00
1
RESTRAINED
THROUGHOUT
1.0
.30
.30
3.80
.24
.30
2.25
10.00
126
1271
5
0
1140
.006
1.6
25.2
2.13
2.37
1.50
3.52
2.00
4.19
2.00
6.18
2.50
0.326
.043
0.305
2.37
57
490
7
10.4
68.8
24.2
2.1
25.0
1FEV
52509
2.0
2.0
0.095
1
23.3
8.26
99.7
0.38
2.15
2.25
739
5.7
83.9
data scaling
XDS
data reduction
AUTOMAR
model building
X-PLOR
refinement
X-PLOR
3.851
data reduction
XDS
phasing
X-PLOR
CRYSTAL STRUCTURE OF THE ALA4AIB MUTATION IN RNASE S
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
A
ALA
5
A
ALA
5
HELX_P
A
LEU
13
A
LEU
13
1
1
9
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
2.015
B
CYS
40
B
SG
CYS
17
1_555
B
CYS
95
B
SG
CYS
72
1_555
disulf
2.030
B
CYS
58
B
SG
CYS
35
1_555
B
CYS
110
B
SG
CYS
87
1_555
disulf
2.030
B
CYS
65
B
SG
CYS
42
1_555
B
CYS
72
B
SG
CYS
49
1_555
covale
1.323
both
A
THR
3
A
C
THR
3
1_555
A
AIB
4
A
N
AIB
4
1_555
covale
1.326
both
A
AIB
4
A
C
AIB
4
1_555
A
ALA
5
A
N
ALA
5
1_555
HYDROLASE
alpha aminoisobutyric acid, AIB, HYDROLASE
B
TYR
92
B
TYR
69
1
B
PRO
93
B
PRO
70
0.02
B
ASN
113
B
ASN
90
1
B
PRO
114
B
PRO
91
0.30
RNAS1_BOVIN
UNP
1
27
P61823
KETAAAKFERQHMDS
RNAS1_BOVIN
UNP
2
50
P61823
NYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQAN
KHIIVACEGNPYVPVHFDASV
27
41
1FEV
1
15
P61823
A
1
1
15
50
150
1FEV
24
124
P61823
B
2
1
101
1
ALA
modified residue
AIB
4
1FEV
A
P61823
UNP
30
4
1
MET
engineered mutation
LEU
13
1FEV
A
P61823
UNP
39
13
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
B
VAL
116
B
VAL
93
B
VAL
124
B
VAL
101
B
TYR
97
B
TYR
74
B
GLU
111
B
GLU
88
B
CYS
72
B
CYS
49
B
GLN
74
B
GLN
51
B
LYS
61
B
LYS
38
B
VAL
63
B
VAL
40
B
VAL
116
B
VAL
93
B
VAL
124
B
VAL
101
B
TYR
97
B
TYR
74
B
GLU
111
B
GLU
88
B
MET
79
B
MET
56
B
GLU
86
B
GLU
63
B
VAL
43
B
VAL
20
B
VAL
47
B
VAL
24
BINDING SITE FOR RESIDUE SO4 B 125
B
SO4
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