12.07
-1.334
1.852
-7.753
A
N
LYS
2
ATOM
A
N
LYS
1
1
1.00
1
N
11.60
-1.943
0.655
-7.101
A
CA
LYS
2
ATOM
A
CA
LYS
1
1
1.00
1
C
11.69
-1.325
0.528
-5.746
A
C
LYS
2
ATOM
A
C
LYS
1
1
1.00
1
C
11.66
-0.084
0.407
-5.672
A
O
LYS
2
ATOM
A
O
LYS
1
1
1.00
1
O
12.71
-1.631
-0.609
-7.915
A
CB
LYS
2
ATOM
A
CB
LYS
1
1
1.00
1
C
15.55
-1.974
-1.892
-7.241
A
CG
LYS
2
ATOM
A
CG
LYS
1
1
1.00
1
C
16.66
-2.102
-3.103
-8.198
A
CD
LYS
2
ATOM
A
CD
LYS
1
1
1.00
1
C
15.73
-0.815
-3.611
-8.824
A
CE
LYS
2
ATOM
A
CE
LYS
1
1
1.00
1
C
13.21
-1.061
-4.900
-9.632
A
NZ
LYS
2
ATOM
A
NZ
LYS
1
1
1.00
1
N
9.76
-2.165
0.536
-4.686
A
N
LEU
3
ATOM
A
N
LEU
1
2
1.00
1
N
8.84
-1.709
0.188
-3.332
A
CA
LEU
3
ATOM
A
CA
LEU
1
2
1.00
1
C
8.55
-2.242
-1.190
-2.970
A
C
LEU
3
ATOM
A
C
LEU
1
2
1.00
1
C
8.36
-3.433
-1.466
-3.093
A
O
LEU
3
ATOM
A
O
LEU
1
2
1.00
1
O
8.38
-2.254
1.169
-2.282
A
CB
LEU
3
ATOM
A
CB
LEU
1
2
1.00
1
C
7.99
-2.026
0.948
-0.760
A
CG
LEU
3
ATOM
A
CG
LEU
1
2
1.00
1
C
7.38
-0.558
1.217
-0.331
A
CD1
LEU
3
ATOM
A
CD1
LEU
1
2
1.00
1
C
7.69
-2.946
1.828
0.075
A
CD2
LEU
3
ATOM
A
CD2
LEU
1
2
1.00
1
C
8.06
-1.364
-2.007
-2.421
A
N
VAL
4
ATOM
A
N
VAL
1
3
1.00
1
N
8.60
-1.802
-3.187
-1.756
A
CA
VAL
4
ATOM
A
CA
VAL
1
3
1.00
1
C
9.07
-1.169
-3.244
-0.378
A
C
VAL
4
ATOM
A
C
VAL
1
3
1.00
1
C
10.22
0.040
-3.304
-0.239
A
O
VAL
4
ATOM
A
O
VAL
1
3
1.00
1
O
7.98
-1.428
-4.429
-2.531
A
CB
VAL
4
ATOM
A
CB
VAL
1
3
1.00
1
C
7.84
-2.051
-5.716
-1.886
A
CG1
VAL
4
ATOM
A
CG1
VAL
1
3
1.00
1
C
8.19
-1.750
-4.301
-4.025
A
CG2
VAL
4
ATOM
A
CG2
VAL
1
3
1.00
1
C
11.83
-2.014
-3.237
0.640
A
N
PHE
5
ATOM
A
N
PHE
1
4
1.00
1
N
12.27
-1.588
-3.380
2.032
A
CA
PHE
5
ATOM
A
CA
PHE
1
4
1.00
1
C
13.82
-2.275
-4.573
2.662
A
C
PHE
5
ATOM
A
C
PHE
1
4
1.00
1
C
15.79
-3.521
-4.672
2.575
A
O
PHE
5
ATOM
A
O
PHE
1
4
1.00
1
O
11.97
-1.980
-2.139
2.822
A
CB
PHE
5
ATOM
A
CB
PHE
1
4
1.00
1
C
11.24
-1.754
-2.267
4.292
A
CG
PHE
5
ATOM
A
CG
PHE
1
4
1.00
1
C
13.30
-0.509
-2.005
4.837
A
CD1
PHE
5
ATOM
A
CD1
PHE
1
4
1.00
1
C
10.94
-2.784
-2.614
5.127
A
CD2
PHE
5
ATOM
A
CD2
PHE
1
4
1.00
1
C
13.41
-0.320
-2.088
6.234
A
CE1
PHE
5
ATOM
A
CE1
PHE
1
4
1.00
1
C
11.77
-2.591
-2.745
6.500
A
CE2
PHE
5
ATOM
A
CE2
PHE
1
4
1.00
1
C
11.58
-1.365
-2.458
7.047
A
CZ
PHE
5
ATOM
A
CZ
PHE
1
4
1.00
1
C
14.81
-1.476
-5.455
3.275
A
N
PHE
6
ATOM
A
N
PHE
1
5
1.00
1
N
15.73
-1.984
-6.541
4.123
A
CA
PHE
6
ATOM
A
CA
PHE
1
5
1.00
1
C
16.89
-1.218
-6.607
5.435
A
C
PHE
6
ATOM
A
C
PHE
1
5
1.00
1
C
13.20
-0.016
-6.875
5.416
A
O
PHE
6
ATOM
A
O
PHE
1
5
1.00
1
O
14.69
-1.848
-7.895
3.449
A
CB
PHE
6
ATOM
A
CB
PHE
1
5
1.00
1
C
17.56
-2.572
-8.988
4.176
A
CG
PHE
6
ATOM
A
CG
PHE
1
5
1.00
1
C
16.39
-3.928
-9.217
3.932
A
CD1
PHE
6
ATOM
A
CD1
PHE
1
5
1.00
1
C
20.27
-1.910
-9.768
5.145
A
CD2
PHE
6
ATOM
A
CD2
PHE
1
5
1.00
1
C
18.91
-4.613
-10.201
4.614
A
CE1
PHE
6
ATOM
A
CE1
PHE
1
5
1.00
1
C
21.33
-2.602
-10.752
5.845
A
CE2
PHE
6
ATOM
A
CE2
PHE
1
5
1.00
1
C
18.84
-3.959
-10.975
5.552
A
CZ
PHE
6
ATOM
A
CZ
PHE
1
5
1.00
1
C
21.78
-1.907
-6.448
6.572
A
N
ALA
7
ATOM
A
N
ALA
1
6
1.00
1
N
23.97
-1.277
-6.712
7.898
A
CA
ALA
7
ATOM
A
CA
ALA
1
6
1.00
1
C
32.80
-2.066
-7.660
8.834
A
C
ALA
7
ATOM
A
C
ALA
1
6
1.00
1
C
29.64
-3.245
-7.905
8.595
A
O
ALA
7
ATOM
A
O
ALA
1
6
1.00
1
O
26.09
-0.953
-5.441
8.593
A
CB
ALA
7
ATOM
A
CB
ALA
1
6
1.00
1
C
33.63
-1.550
-8.249
9.820
A
OXT
ALA
7
ATOM
A
OXT
ALA
1
6
1.00
1
O
35.51
-3.334
-11.524
9.718
A
C
ACT
1008
HETATM
B
C
ACT
2
1.00
1
C
36.47
-3.296
-12.741
10.153
A
O
ACT
1008
HETATM
B
O
ACT
2
1.00
1
O
26.04
-4.406
-10.873
9.502
A
OXT
ACT
1008
HETATM
B
OXT
ACT
2
1.00
1
O
27.90
-2.025
-10.826
9.449
A
CH3
ACT
1008
HETATM
B
CH3
ACT
2
1.00
1
C
36.53
-2.149
4.522
-7.326
A
O
HOH
2001
HETATM
C
O
HOH
3
1.00
1
O
39.72
-3.671
-6.911
-8.668
A
O
HOH
2002
HETATM
C
O
HOH
3
1.00
1
O
25.69
-1.183
-14.039
10.669
A
O
HOH
2003
HETATM
C
O
HOH
3
1.00
1
O
0.104384
0.000000
0.000000
0.000000
0.084388
0.000000
0.000000
0.000000
0.023546
0.00000
0.00000
0.00000
Colletier, J.
Laganowsky, A.
Sawaya, M.R.
Eisenberg, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
9.580
11.850
42.470
C2 H3 O2 -1
59.044
ACETATE ION
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
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 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
108
16938
10.1073/PNAS.1112600108
21949245
Molecular Basis for Amyloid-{Beta} Polymorphism.
2011
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
MARMOSAIC 225 mm CCD
SINGLE WAVELENGTH
M
x-ray
1
0.87260
1.0
ID23-2
ESRF
0.87260
SYNCHROTRON
ESRF BEAMLINE ID23-2
724.909
AMYLOID BETA A4 PROTEIN
SEGMENT KLVFFA, RESIDUES 687-692
1
syn
polymer
59.044
ACETATE ION
1
syn
non-polymer
18.015
water
3
nat
water
AMYLOID BETA PEPTIDE, ABPP, APPI, APP, ALZHEIMER DISEASE AMYLOID PROTEIN, CEREBRAL VASCULAR AMYLOID PEPTIDE, CVAP, PREA4, PROTEASE NEXIN-II, PN-II
no
no
KLVFFA
KLVFFA
A
polypeptide(L)
n
n
n
n
n
n
1
1.71
28
NONE
5.5
AB16-21 FORM I CRYSTALS WERE OBTAINED AFTER THE SEGMENT WAS DISSOLVED IN WATER AT 5 MG/ML AND MIXED WITH 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 5.5, 45 % V/V MPD
repository
Initial release
1
0
2011-10-26
AFTER 3NS
BOVINE TRYPSIN COMPLEXED TO APPI
STRUCTURE OF SEGMENT AIIGLM FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 30-35)
SOLUTION STRUCTURE OF CAPPD*, AN INDEPENDENTLY FOLDEDEXTRACELLULAR DOMAIN OF HUMAN AMYLOID-BETA PRECURSORPROTEIN
AMYLOID BETA PEPTIDE (25-35), NMR, 20 STRUCTURES
SOLUTION STRUCTURE OF THE METHIONINE-OXIDIZED AMYLOID BETA-PEPTIDE (1-40). DOES OXIDATION AFFECT CONFORMATIONAL SWITCHING? NMR, 10 STRUCTURES
SOLUTION STRUCTURE OF FRAGMENT (25-35) OF BETA AMYLOIDPEPTIDE IN SDS MICELLAR SOLUTION
SOLUTION NMR STRUCTURE OF AMYLOID BETA[E16], RESIDUES 1-28, 14 STRUCTURES
STRUCTURE OF SEGMENT MVGGVVIA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 35-42), ALTERNATE POLYMORPH 2
STRUCTURE OF SEGMENT MVGGVVIA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 35-42), ALTERNATE POLYMORPH 1
BOVINE CHYMOTRYPSIN COMPLEXED TO APPI
AFTER 2NS
THE SOLUTION STRUCTURE OF AMYLOID BETA-PEPTIDE (1-40 ) IN A WATER-MICELLE ENVIRONMENT. IS THE MEMBRANE- SPANNING DOMAIN WHERE WE THINK IT IS? NMR, 10 STRUCTURES
CRYSTAL STRUCTURE OF HUMAN INSULIN-DEGRADING ENZYME IN COMPLEX WITH AMYLOID-BETA (1-42)
X11 PTB DOMAIN
NMR ANALYSIS OF 25-35 FRAGMENT OF BETA AMYLOID PEPTIDE
ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE COMPLEXED WITH A ZINC (II) CATION
NMR STRUCTURE OF THE FRAGMENT 25-35 OF BETA AMYLOID PEPTIDEIN 20/80 V:V HEXAFLUOROISOPROPANOL/WATER MIXTURE
SOLUTION STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (1-42)
ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN WATER SOLUTION AT PH 6.5
3D STRUCTURE OF ALZHEIMER'S ABETA(1-42) FIBRILS
AFTER 4NS
ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (RESIDUES 1 - 28) (NMR, MINIMIZED AVERAGE STRUCTURE)
HUMAN APP CORE DOMAIN
MOLECULAR DYNAMICS SIMULATION OF AMYLOID BETA 1-42 ( PDB: 1IYT) IN WATER
STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID PRECURSORPROTEIN COPPER BINDING DOMAIN
THE ALZHEIMER'S DISEASE AMYLOID A4 PEPTIDE (RESIDUES 1 -40)
ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (RESIDUES 1 - 28) (NMR, 5 STRUCTURES)
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH KUNITZ PROTEASE INHIBITOR DOMAINOF PROTEASE NEXIN II
ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN TFE-WATER (80-20) SOLUTION
MODEL OF ALZHEIMER'S DISEASE AMYLOID-SS PEPTIDE BASED ON A RNA BINDING PROTEIN
SOLUTION NMR STRUCTURE OF AMYLOID BETA[F16], RESIDUES 1-28, 15 STRUCTURES
STRUCTURE OF SEGMENT KLVFFA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 16-21), ALTERNATE POLYMORPH III
N-TERMINAL DOMAIN OF THE AMYLOID PRECURSOR PROTEIN
ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10- 35)
PDBE
Y
PDBE
2010-12-14
REL
ACT
ACETATE ION
HOH
water
9606
HUMAN
HOMO SAPIENS
sample
IN VIVO AMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTIC PRODUCT OF
THE AMYLOID PRECURSOR PROTEIN (APP). AB SEGMENT 16-KLVFFA-21
CORRESPONDS TO RESIDUES 687-692 OF APP
ACT
1008
2
ACT
ACT
1008
A
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
LYS
2
n
1
LYS
2
A
LEU
3
n
2
LEU
3
A
VAL
4
n
3
VAL
4
A
PHE
5
n
4
PHE
5
A
PHE
6
n
5
PHE
6
A
ALA
7
n
6
ALA
7
A
author_and_software_defined_assembly
PISA
1
monomeric
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
A
A
O
O
HOH
HOH
2001
2002
2.07
1_555
1_565
16.442
-4.28
0.00
0.00
22.62
0.00
-18.34
0.946
0.962
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
0.24787
0.20640
0.20837
1.91
11.41
20
372
5.1
85.03
2.823
0.074
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.059
0.043
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.91
11.41
3
59
4
0
52
0.020
0.023
56
1.703
2.029
73
10.614
5.000
5
4.237
20.000
2
11.363
15.000
9
0.121
0.200
8
0.009
0.020
42
0.226
1.954
12
20
40.63
19.348
1.90
21.20
2Y2A
392
3.5
0.15
1
7.40
3.5
85.0
0.36
1.90
2.20
3.85
1
3.9
75.7
refinement
REFMAC
5.6.0081
data reduction
XDS
data scaling
XSCALE
phasing
PHASER
AMYLOID BETA A4 PROTEIN
Structure of segment KLVFFA from the amyloid-beta peptide (Ab, residues 16-21), alternate polymorph I
1
N
N
2
N
N
3
N
N
PROTEIN FIBRIL
PROTEIN FIBRIL, ALZHEIMER DISEASE
A4_HUMAN
UNP
1
P05067
687
692
2Y2A
2
7
P05067
A
1
1
6
BINDING SITE FOR RESIDUE ACT A 1008
Software
5
A
LYS
2
A
LYS
1
5
4_435
A
LYS
2
A
LYS
1
5
2_445
A
PHE
6
A
PHE
5
5
1_555
A
ALA
7
A
ALA
6
5
1_555
A
HOH
2003
C
HOH
5
1_555
19
P 21 21 21