0.036303
0.000000
0.000000
0.000000
0.032240
0.000000
0.000000
0.000000
0.208160
0.000000
0.000000
0.000000
Apostol, M.I.
Sawaya, M.R.
Eisenberg, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
27.546
31.017
4.804
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 H14 O2
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
N
1
N
N
N
2
N
C
N
3
N
C
N
4
N
O
N
5
N
O
N
6
N
H
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
N
N
12
S
C
N
13
N
C
N
14
N
O
N
15
N
C
Y
16
N
C
Y
17
N
N
Y
18
N
C
Y
19
N
C
Y
20
N
N
N
21
N
O
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
N
N
33
S
C
N
34
N
C
N
35
N
O
N
36
S
C
N
37
N
C
N
38
N
C
N
39
N
C
N
40
N
O
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
C
N
55
N
C
N
56
N
O
N
57
N
C
N
58
N
C
N
59
S
C
N
60
N
O
N
61
N
C
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
N
N
77
S
C
N
78
N
C
N
79
N
O
N
80
N
C
Y
81
N
C
Y
82
N
C
Y
83
N
C
Y
84
N
C
Y
85
N
C
Y
86
N
C
N
87
N
O
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
N
N
100
S
C
N
101
N
C
N
102
N
O
N
103
N
C
N
104
N
O
N
105
N
O
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
doub
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
Y
21
N
sing
Y
22
N
doub
Y
23
N
doub
N
24
N
sing
Y
25
N
sing
N
26
N
sing
Y
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
doub
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
Y
84
N
doub
Y
85
N
sing
Y
86
N
sing
N
87
N
sing
Y
88
N
doub
N
89
N
sing
Y
90
N
doub
N
91
N
sing
Y
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
50
2456
2463
10.1021/bi101803k
21323366
Atomic structures suggest determinants of transmission barriers in Mammalian prion disease.
2011
10.2210/pdb3nvf/pdb
pdb_00003nvf
100
1
CCD
2008-01-01
MAR CCD 225
SINGLE WAVELENGTH
M
x-ray
1
0.8726
1.0
ID13
ESRF
0.8726
SYNCHROTRON
ESRF BEAMLINE ID13
673.781
Major prion protein
1
syn
polymer
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
1
syn
non-polymer
PrP, PrP27-30, PrP33-35C, ASCR
no
no
IIHFGS
IIHFGS
A
polypeptide(L)
n
n
n
n
n
n
1
1.52
19.23
VAPOR DIFFUSION, HANGING DROP
7.4
100mM Tris pH 7.4, 25% MPD, vapor diffusion, hanging drop, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2011-03-02
1
1
2011-07-13
1
2
2024-02-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
MMHFGN hexapeptide (residues 138-143) from golden hamster prion protein
MIHFGN hexapeptide (residues 137-142) from mouse prion protein
MIHFGND (residues 137-143) from mouse prion protein
RCSB
Y
RCSB
2010-07-08
REL
REL
MPD
(4S)-2-METHYL-2,4-PENTANEDIOL
IIHFGS (UNP residues 138-143) from human prion
9606
human
Homo sapiens
sample
MPD
1
2
MPD
MPD
7
A
2.200
2.200
20.600
20.600
Phaser MODE: MR_AUTO
ILE
1
n
1
ILE
1
A
ILE
2
n
2
ILE
2
A
HIS
3
n
3
HIS
3
A
PHE
4
n
4
PHE
4
A
GLY
5
n
5
GLY
5
A
SER
6
n
6
SER
6
A
author_defined_assembly
10
decameric
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
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_557
x,y,z+2
crystal symmetry operation
0.0000000000
0.0000000000
9.6080000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_556
x,y,z+1
crystal symmetry operation
0.0000000000
0.0000000000
4.8040000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_554
x,y,z-1
crystal symmetry operation
0.0000000000
0.0000000000
-4.8040000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_553
x,y,z-2
crystal symmetry operation
0.0000000000
0.0000000000
-9.6080000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_657
-x+1,-y,z+2
crystal symmetry operation
27.5460000000
0.0000000000
9.6080000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_656
-x+1,-y,z+1
crystal symmetry operation
27.5460000000
0.0000000000
4.8040000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_655
-x+1,-y,z
crystal symmetry operation
27.5460000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_654
-x+1,-y,z-1
crystal symmetry operation
27.5460000000
0.0000000000
-4.8040000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_653
-x+1,-y,z-2
crystal symmetry operation
27.5460000000
0.0000000000
-9.6080000000
52.980
20.8202
10.200
1.0000
0.0000
0.0000
-0.0400
0.0000
-0.9500
0.9550
0.9400
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.2263
0.2118
0.2133
1.8000
20.6000
40
433
9.2000
86.4300
0.2521
0.2013
1.000
1.000
0.8682
4.0090
0.1110
0.2379
0.1668
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.1670
0.8000
0.8000
1.4000
MAXIMUM LIKELIHOOD
MASK
1.8000
20.6000
0
56
8
0
48
0.009
0.021
56
0.001
0.020
35
1.657
2.043
75
0.693
3.000
84
9.100
5.000
5
52.201
20.000
2
10.817
15.000
7
0.053
0.200
8
0.004
0.020
52
0.001
0.020
12
0.523
1.500
29
0.157
1.500
12
0.853
2.000
46
1.220
3.000
27
1.673
4.500
29
0.3300
0.3820
2.0110
4
87
91
5
72.2200
1.800
90.000
3NVF
443
0.216
1.137
1
6.800
3.800
85.400
0.395
1.800
1.940
63
1.424
1.700
67.000
0.327
1.940
2.130
83
1.294
2.300
85.600
0.314
2.130
2.440
89
0.964
3.200
78.800
0.244
2.440
3.080
87
1.062
5.400
100.000
0.197
3.080
90.000
121
1.199
5.100
94.500
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
program
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
program
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Wed Feb 15 11:59:26 2006
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
1.3.2
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
IIHFGS segment 138-143 from human prion
1
N
N
2
N
N
PROTEIN FIBRIL
amyloid-like protofibril, PROTEIN FIBRIL
PRIO_HUMAN
UNP
1
138
P04156
IIHFGS
138
143
3NVF
1
6
P04156
A
1
1
6
BINDING SITE FOR RESIDUE MPD A 7
A
MPD
7
Software
5
A
ILE
1
A
ILE
1
5
4_444
A
ILE
2
A
ILE
2
5
4_444
A
HIS
3
A
HIS
3
5
1_555
A
HIS
3
A
HIS
3
5
1_554
A
PHE
4
A
PHE
4
5
3_544
18
P 21 21 2