0.024809
0.000000
0.000000
0.000000
0.021328
0.000000
0.000000
0.000000
0.020040
0.00000
0.00000
0.00000
De Vos, S.
Backmann, J.
Steyaert, J.
Loris, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.0
90.0
90.0
40.308
46.886
49.901
C10 H14 N5 O8 P
363.221
GUANOSINE-2'-MONOPHOSPHATE
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
Ca 2
40.078
CALCIUM ION
non-polymer
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
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
Biochemistry
BICHAW
0033
0006-2960
40
10140
10149
10.1021/bi010565n
11513591
Hydrophobic core manipulations in ribonuclease T1
2001
10.2210/pdb1i3f/pdb
pdb_00001i3f
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293
1
IMAGE PLATE
1999-08-14
MARRESEARCH
graphite
SINGLE WAVELENGTH
M
x-ray
1
0.909
1.0
X11
EMBL/DESY, HAMBURG
0.909
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
11082.641
GUANYL-SPECIFIC RIBONUCLEASE T1
3.1.27.3
V89S, Q25K
1
man
polymer
40.078
CALCIUM ION
1
syn
non-polymer
363.221
GUANOSINE-2'-MONOPHOSPHATE
1
syn
non-polymer
18.015
water
45
nat
water
RNASE T1
no
no
ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVF
NENNQLAGSITHTGASGNNFVECT
ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVF
NENNQLAGSITHTGASGNNFVECT
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
Aspergillus
Escherichia
sample
5062
Aspergillus oryzae
562
Escherichia coli
1
2.13
42.18
VAPOR DIFFUSION, HANGING DROP
4.2
MPD, sodium acetate, calcium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
database_2
diffrn_source
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-03-07
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RIBONUCLEASE T1 V16A MUTANT, FORM I
RIBONUCLEASE T1 V16A MUTANT, FORM II
RIBONUCLEASE T1 V16T MUTANT
Ribonuclease T1 V78T mutant
RCSB
Y
RCSB
2001-02-15
REL
REL
CA
CALCIUM ION
2GP
GUANOSINE-2'-MONOPHOSPHATE
HOH
water
CA
105
2
CA
CA
105
A
2GP
106
3
2GP
2GP
106
A
HOH
201
4
HOH
HOH
201
A
HOH
202
4
HOH
HOH
202
A
HOH
203
4
HOH
HOH
203
A
HOH
204
4
HOH
HOH
204
A
HOH
205
4
HOH
HOH
205
A
HOH
206
4
HOH
HOH
206
A
HOH
207
4
HOH
HOH
207
A
HOH
208
4
HOH
HOH
208
A
HOH
209
4
HOH
HOH
209
A
HOH
210
4
HOH
HOH
210
A
HOH
211
4
HOH
HOH
211
A
HOH
212
4
HOH
HOH
212
A
HOH
213
4
HOH
HOH
213
A
HOH
214
4
HOH
HOH
214
A
HOH
215
4
HOH
HOH
215
A
HOH
216
4
HOH
HOH
216
A
HOH
217
4
HOH
HOH
217
A
HOH
218
4
HOH
HOH
218
A
HOH
219
4
HOH
HOH
219
A
HOH
220
4
HOH
HOH
220
A
HOH
221
4
HOH
HOH
221
A
HOH
222
4
HOH
HOH
222
A
HOH
223
4
HOH
HOH
223
A
HOH
224
4
HOH
HOH
224
A
HOH
225
4
HOH
HOH
225
A
HOH
226
4
HOH
HOH
226
A
HOH
227
4
HOH
HOH
227
A
HOH
228
4
HOH
HOH
228
A
HOH
229
4
HOH
HOH
229
A
HOH
230
4
HOH
HOH
230
A
HOH
231
4
HOH
HOH
231
A
HOH
232
4
HOH
HOH
232
A
HOH
233
4
HOH
HOH
233
A
HOH
234
4
HOH
HOH
234
A
HOH
235
4
HOH
HOH
235
A
HOH
236
4
HOH
HOH
236
A
HOH
237
4
HOH
HOH
237
A
HOH
238
4
HOH
HOH
238
A
HOH
239
4
HOH
HOH
239
A
HOH
240
4
HOH
HOH
240
A
HOH
241
4
HOH
HOH
241
A
HOH
242
4
HOH
HOH
242
A
HOH
243
4
HOH
HOH
243
A
HOH
244
4
HOH
HOH
244
A
HOH
245
4
HOH
HOH
245
A
ALA
1
n
1
ALA
1
A
CYS
2
n
2
CYS
2
A
ASP
3
n
3
ASP
3
A
TYR
4
n
4
TYR
4
A
THR
5
n
5
THR
5
A
CYS
6
n
6
CYS
6
A
GLY
7
n
7
GLY
7
A
SER
8
n
8
SER
8
A
ASN
9
n
9
ASN
9
A
CYS
10
n
10
CYS
10
A
TYR
11
n
11
TYR
11
A
SER
12
n
12
SER
12
A
SER
13
n
13
SER
13
A
SER
14
n
14
SER
14
A
ASP
15
n
15
ASP
15
A
VAL
16
n
16
VAL
16
A
SER
17
n
17
SER
17
A
THR
18
n
18
THR
18
A
ALA
19
n
19
ALA
19
A
GLN
20
n
20
GLN
20
A
ALA
21
n
21
ALA
21
A
ALA
22
n
22
ALA
22
A
GLY
23
n
23
GLY
23
A
TYR
24
n
24
TYR
24
A
LYS
25
n
25
LYS
25
A
LEU
26
n
26
LEU
26
A
HIS
27
n
27
HIS
27
A
GLU
28
n
28
GLU
28
A
ASP
29
n
29
ASP
29
A
GLY
30
n
30
GLY
30
A
GLU
31
n
31
GLU
31
A
THR
32
n
32
THR
32
A
VAL
33
n
33
VAL
33
A
GLY
34
n
34
GLY
34
A
SER
35
n
35
SER
35
A
ASN
36
n
36
ASN
36
A
SER
37
n
37
SER
37
A
TYR
38
n
38
TYR
38
A
PRO
39
n
39
PRO
39
A
HIS
40
n
40
HIS
40
A
LYS
41
n
41
LYS
41
A
TYR
42
n
42
TYR
42
A
ASN
43
n
43
ASN
43
A
ASN
44
n
44
ASN
44
A
TYR
45
n
45
TYR
45
A
GLU
46
n
46
GLU
46
A
GLY
47
n
47
GLY
47
A
PHE
48
n
48
PHE
48
A
ASP
49
n
49
ASP
49
A
PHE
50
n
50
PHE
50
A
SER
51
n
51
SER
51
A
VAL
52
n
52
VAL
52
A
SER
53
n
53
SER
53
A
SER
54
n
54
SER
54
A
PRO
55
n
55
PRO
55
A
TYR
56
n
56
TYR
56
A
TYR
57
n
57
TYR
57
A
GLU
58
n
58
GLU
58
A
TRP
59
n
59
TRP
59
A
PRO
60
n
60
PRO
60
A
ILE
61
n
61
ILE
61
A
LEU
62
n
62
LEU
62
A
SER
63
n
63
SER
63
A
SER
64
n
64
SER
64
A
GLY
65
n
65
GLY
65
A
ASP
66
n
66
ASP
66
A
VAL
67
n
67
VAL
67
A
TYR
68
n
68
TYR
68
A
SER
69
n
69
SER
69
A
GLY
70
n
70
GLY
70
A
GLY
71
n
71
GLY
71
A
SER
72
n
72
SER
72
A
PRO
73
n
73
PRO
73
A
GLY
74
n
74
GLY
74
A
ALA
75
n
75
ALA
75
A
ASP
76
n
76
ASP
76
A
ARG
77
n
77
ARG
77
A
VAL
78
n
78
VAL
78
A
VAL
79
n
79
VAL
79
A
PHE
80
n
80
PHE
80
A
ASN
81
n
81
ASN
81
A
GLU
82
n
82
GLU
82
A
ASN
83
n
83
ASN
83
A
ASN
84
n
84
ASN
84
A
GLN
85
n
85
GLN
85
A
LEU
86
n
86
LEU
86
A
ALA
87
n
87
ALA
87
A
GLY
88
n
88
GLY
88
A
SER
89
n
89
SER
89
A
ILE
90
n
90
ILE
90
A
THR
91
n
91
THR
91
A
HIS
92
n
92
HIS
92
A
THR
93
n
93
THR
93
A
GLY
94
n
94
GLY
94
A
ALA
95
n
95
ALA
95
A
SER
96
n
96
SER
96
A
GLY
97
n
97
GLY
97
A
ASN
98
n
98
ASN
98
A
ASN
99
n
99
ASN
99
A
PHE
100
n
100
PHE
100
A
VAL
101
n
101
VAL
101
A
GLU
102
n
102
GLU
102
A
CYS
103
n
103
CYS
103
A
THR
104
n
104
THR
104
A
author_defined_assembly
1
monomeric
A
ASP
15
A
OD2
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
A
ASP
15
A
OD1
ASP
15
1_555
49.1
A
ASP
15
A
OD2
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
201
D
O
HOH
1_555
147.5
A
ASP
15
A
OD1
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
201
D
O
HOH
1_555
150.5
A
ASP
15
A
OD2
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
204
D
O
HOH
1_555
77.4
A
ASP
15
A
OD1
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
204
D
O
HOH
1_555
76.0
A
HOH
201
D
O
HOH
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
204
D
O
HOH
1_555
124.3
A
ASP
15
A
OD2
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
212
D
O
HOH
1_555
77.1
A
ASP
15
A
OD1
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
212
D
O
HOH
1_555
124.1
A
HOH
201
D
O
HOH
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
212
D
O
HOH
1_555
83.5
A
HOH
204
D
O
HOH
1_555
A
CA
105
B
CA
CA
1_555
A
HOH
212
D
O
HOH
1_555
79.2
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
CYS
6
A
N
CYS
6
A
O
ASN
9
A
O
ASN
9
A
N
TYR
42
A
N
TYR
42
A
O
TYR
56
A
O
TYR
56
A
O
TRP
59
A
O
TRP
59
A
N
VAL
78
A
N
VAL
78
A
O
VAL
79
A
O
VAL
79
A
N
ALA
87
A
N
ALA
87
A
N
THR
91
A
N
THR
91
A
O
VAL
101
A
O
VAL
101
1
A
CD
LYS
25
A
CD
LYS
25
1
Y
1
A
CE
LYS
25
A
CE
LYS
25
1
Y
1
A
NZ
LYS
25
A
NZ
LYS
25
1
Y
1
A
CD
LYS
41
A
CD
LYS
41
1
Y
1
A
CE
LYS
41
A
CE
LYS
41
1
Y
1
A
NZ
LYS
41
A
NZ
LYS
41
1
Y
1
A
CG
ASP
49
A
CG
ASP
49
1
Y
1
A
OD1
ASP
49
A
OD1
ASP
49
1
Y
1
A
OD2
ASP
49
A
OD2
ASP
49
1
Y
1
9.50
1.50
119.30
128.80
A
A
A
C
N
CA
SER
PRO
PRO
72
73
73
Y
1
A
SER
37
51.35
79.23
1
A
SER
69
-142.85
30.80
1
A
ASN
84
73.62
42.25
0.2834
0.173
0.1897
0.1897
2.35
2.43
635
4178
4178
random
1
0
0
MOLECULAR REPLACEMENT
Engh & Huber
2.35
2.43
45
842
25
0
772
0.008
1.493
14.1
2.35
20.0
1I3F
4178
4178
-6
-3
0.151
1
7.11
3.22
98.6
0.406
2.35
2.43
3.13
383
3.25
97.7
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
X-PLOR
3.851
Ribonuclease T1 V89S mutant
1
N
N
2
N
N
3
N
N
4
N
N
A
SER
12
A
SER
12
HELX_P
A
GLY
30
A
GLY
30
1
1
19
disulf
2.023
A
CYS
2
A
SG
CYS
2
1_555
A
CYS
10
A
SG
CYS
10
1_555
disulf
2.024
A
CYS
6
A
SG
CYS
6
1_555
A
CYS
103
A
SG
CYS
103
1_555
metalc
2.561
A
ASP
15
A
OD2
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
metalc
2.725
A
ASP
15
A
OD1
ASP
15
1_555
A
CA
105
B
CA
CA
1_555
metalc
2.661
A
CA
105
B
CA
CA
1_555
A
HOH
201
D
O
HOH
1_555
metalc
2.735
A
CA
105
B
CA
CA
1_555
A
HOH
204
D
O
HOH
1_555
metalc
2.436
A
CA
105
B
CA
CA
1_555
A
HOH
212
D
O
HOH
1_555
HYDROLASE
ribonuclease, hydrophobic core, cavity creation, hydrophobic effect, HYDROLASE
A
TYR
38
A
TYR
38
1
A
PRO
39
A
PRO
39
-0.32
A
SER
54
A
SER
54
1
A
PRO
55
A
PRO
55
-0.10
RNT1_ASPOR
UNP
1
27
P00651
ACDYTCGSNCYSSSDVSTAQAAGYQLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVF
NENNQLAGVITHTGASGNNFVECT
27
130
1I3F
1
104
P00651
A
1
1
104
1
GLN
engineered mutation
LYS
25
1I3F
A
P00651
UNP
51
25
1
VAL
engineered mutation
SER
89
1I3F
A
P00651
UNP
115
89
2
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
4
A
TYR
4
A
CYS
6
A
CYS
6
A
ASN
9
A
ASN
9
A
TYR
11
A
TYR
11
A
HIS
40
A
HIS
40
A
TYR
42
A
TYR
42
A
TYR
56
A
TYR
56
A
PRO
60
A
PRO
60
A
ASP
76
A
ASP
76
A
ASN
81
A
ASN
81
A
LEU
86
A
LEU
86
A
THR
91
A
THR
91
A
VAL
101
A
VAL
101
A
GLU
102
A
GLU
102
BINDING SITE FOR RESIDUE CA A 105
A
CA
105
Software
4
BINDING SITE FOR RESIDUE 2GP A 106
A
2GP
106
Software
11
A
ASP
15
A
ASP
15
4
1_555
A
HOH
201
D
HOH
4
1_555
A
HOH
204
D
HOH
4
1_555
A
HOH
212
D
HOH
4
1_555
A
TYR
38
A
TYR
38
11
1_555
A
HIS
40
A
HIS
40
11
1_555
A
LYS
41
A
LYS
41
11
1_555
A
TYR
42
A
TYR
42
11
1_555
A
ASN
43
A
ASN
43
11
1_555
A
ASN
44
A
ASN
44
11
1_555
A
TYR
45
A
TYR
45
11
1_555
A
GLU
46
A
GLU
46
11
1_555
A
GLU
58
A
GLU
58
11
1_555
A
ASN
98
A
ASN
98
11
1_555
A
PHE
100
A
PHE
100
11
1_555
19
P 21 21 21