1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Wang, D.C.
Gao, G.H.
Shao, F.
Dai, J.X.
Wang, J.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
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
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
10973
10978
10.1021/bi010167k
11551192
Solution structure of PAFP-S: a new knottin-type antifungal peptide from the seeds of Phytolacca americana
2001
10.2210/pdb1dkc/pdb
pdb_00001dkc
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3939.489
ANTIFUNGAL PEPTIDE
1
nat
polymer
PAFP-S
no
no
AGCIKNGGRCNASAGPPYCCSSYCFQIAGQSYGVCKNR
AGCIKNGGRCNASAGPPYCCSSYCFQIAGQSYGVCKNR
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
American pokeweed
SEED
Phytolacca
sample
3527
Phytolacca americana
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-12-13
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
RCSB
Y
RCSB
1999-12-07
REL
REL
THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES
structures with the lowest energy
30
10
2D NOESY
DQF-COSY
2D COSY
2D TOCSY
E-COSY
2D NOESY
NA
3.5
AMBIENT
300
K
SIMULATED ANNEALING MOLECULAR DYNAMICS
1
closest to the average
4MM PROTEIN, 0.2 MM DSS
4MM PROTEIN, 0.2 MM DSS
BRUKER
collection
UXNMR
1.0
BIOSYM
processing
Felix
97
BRUNGER
refinement
X-PLOR
3.851
600
Bruker
DMX
ALA
1
n
1
ALA
1
A
GLY
2
n
2
GLY
2
A
CYS
3
n
3
CYS
3
A
ILE
4
n
4
ILE
4
A
LYS
5
n
5
LYS
5
A
ASN
6
n
6
ASN
6
A
GLY
7
n
7
GLY
7
A
GLY
8
n
8
GLY
8
A
ARG
9
n
9
ARG
9
A
CYS
10
n
10
CYS
10
A
ASN
11
n
11
ASN
11
A
ALA
12
n
12
ALA
12
A
SER
13
n
13
SER
13
A
ALA
14
n
14
ALA
14
A
GLY
15
n
15
GLY
15
A
PRO
16
n
16
PRO
16
A
PRO
17
n
17
PRO
17
A
TYR
18
n
18
TYR
18
A
CYS
19
n
19
CYS
19
A
CYS
20
n
20
CYS
20
A
SER
21
n
21
SER
21
A
SER
22
n
22
SER
22
A
TYR
23
n
23
TYR
23
A
CYS
24
n
24
CYS
24
A
PHE
25
n
25
PHE
25
A
GLN
26
n
26
GLN
26
A
ILE
27
n
27
ILE
27
A
ALA
28
n
28
ALA
28
A
GLY
29
n
29
GLY
29
A
GLN
30
n
30
GLN
30
A
SER
31
n
31
SER
31
A
TYR
32
n
32
TYR
32
A
GLY
33
n
33
GLY
33
A
VAL
34
n
34
VAL
34
A
CYS
35
n
35
CYS
35
A
LYS
36
n
36
LYS
36
A
ASN
37
n
37
ASN
37
A
ARG
38
n
38
ARG
38
A
author_defined_assembly
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
A
N
CYS
10
A
N
CYS
10
A
O
GLY
33
A
O
GLY
33
A
O
LYS
36
A
O
LYS
36
A
N
TYR
23
A
N
TYR
23
1
A
O
ARG
38
A
O
ARG
38
1
Y
2
A
O
ARG
38
A
O
ARG
38
1
Y
3
A
O
ARG
38
A
O
ARG
38
1
Y
4
A
O
ARG
38
A
O
ARG
38
1
Y
5
A
O
ARG
38
A
O
ARG
38
1
Y
6
A
O
ARG
38
A
O
ARG
38
1
Y
7
A
O
ARG
38
A
O
ARG
38
1
Y
8
A
O
ARG
38
A
O
ARG
38
1
Y
9
A
O
ARG
38
A
O
ARG
38
1
Y
10
A
O
ARG
38
A
O
ARG
38
1
Y
1
A
A
HZ3
OG
LYS
SER
5
21
1.31
1
A
A
HZ2
OD1
LYS
ASN
36
37
1.33
1
A
A
OD1
HZ1
ASN
LYS
6
36
1.34
1
A
A
OG
HH22
SER
ARG
22
38
1.38
1
A
A
HG
OG
SER
SER
13
31
1.39
1
A
A
H
O
PHE
VAL
25
34
1.47
1
A
A
HZ2
O
LYS
CYS
5
20
1.53
1
A
A
O
H
GLY
CYS
8
35
1.54
1
A
A
HH12
OD1
ARG
ASN
9
11
1.55
2
A
A
O
HZ3
CYS
LYS
3
5
1.36
2
A
A
OD1
HZ3
ASN
LYS
6
36
1.44
2
A
A
O
HH
GLY
TYR
2
18
1.45
2
A
A
H
O
PHE
VAL
25
34
1.51
2
A
A
HG
OD1
SER
ASN
21
37
1.55
2
A
A
O
HG
SER
SER
21
22
1.57
3
A
A
OD1
HZ3
ASN
LYS
6
36
1.35
3
A
A
HZ1
OD1
LYS
ASN
36
37
1.35
3
A
A
HG
O
SER
LYS
21
36
1.43
3
A
A
HZ3
O
LYS
CYS
5
20
1.44
3
A
A
O
HH22
GLY
ARG
7
9
1.47
3
A
A
O
HH
ALA
TYR
28
32
1.49
3
A
A
H
O
PHE
VAL
25
34
1.52
3
A
A
O
H
GLY
CYS
8
35
1.55
3
A
A
O
HG
SER
SER
21
22
1.55
4
A
A
HZ1
OD1
LYS
ASN
5
6
1.37
4
A
A
O
HZ2
LYS
LYS
5
36
1.39
4
A
A
HZ3
OD1
LYS
ASN
36
37
1.47
4
A
A
O
HH21
GLY
ARG
7
9
1.47
4
A
A
O
HH
GLY
TYR
2
18
1.49
4
A
A
H
O
PHE
VAL
25
34
1.49
5
A
A
HZ2
OD1
LYS
ASN
5
37
1.35
5
A
A
OD1
HZ2
ASN
LYS
6
36
1.37
5
A
A
O
HH21
SER
ARG
22
38
1.48
5
A
A
H
OE1
ALA
GLN
12
26
1.48
5
A
A
H
O
PHE
VAL
25
34
1.50
5
A
A
O
HG
LYS
SER
5
21
1.56
5
A
A
O
H
GLY
CYS
8
35
1.56
5
A
A
HD22
O
ASN
SER
11
31
1.58
5
A
A
O
H
PHE
VAL
25
34
1.59
6
A
A
HZ3
OG
LYS
SER
5
21
1.30
6
A
A
OD1
HZ3
ASN
LYS
6
36
1.40
6
A
A
H
OE1
ALA
GLN
12
26
1.45
6
A
A
H
O
PHE
VAL
25
34
1.48
6
A
A
O
HH11
GLY
ARG
8
9
1.50
6
A
A
OD1
HG
ASN
SER
11
31
1.57
6
A
A
HD22
OD1
ASN
ASN
6
37
1.60
7
A
A
HZ1
OD1
LYS
ASN
5
6
1.34
7
A
A
OG
HH21
SER
ARG
22
38
1.42
7
A
A
O
HH
GLY
TYR
2
18
1.46
7
A
A
H
O
PHE
VAL
25
34
1.48
7
A
A
HD21
OG
ASN
SER
11
31
1.49
7
A
A
O
HH21
GLY
ARG
8
9
1.49
7
A
A
HE
O
ARG
GLY
9
33
1.52
8
A
A
HZ1
OD1
LYS
ASN
5
37
1.34
8
A
A
HZ2
OD1
LYS
ASN
5
6
1.35
8
A
A
OG
HH22
SER
ARG
22
38
1.41
8
A
A
OD1
HG
ASN
SER
11
31
1.45
8
A
A
H
O
PHE
VAL
25
34
1.51
8
A
A
O
HH12
SER
ARG
22
38
1.53
8
A
A
HG
O
SER
ASN
21
37
1.54
9
A
A
HZ3
OD1
LYS
ASN
5
6
1.34
9
A
A
HZ3
OD1
LYS
ASN
36
37
1.36
9
A
A
O
HH
GLY
TYR
2
18
1.45
9
A
A
H
O
PHE
VAL
25
34
1.50
9
A
A
HH11
O
ARG
GLY
9
33
1.57
10
A
A
OD1
HZ1
ASN
LYS
6
36
1.34
10
A
A
O
HH
ALA
TYR
1
18
1.44
10
A
A
HG
O
SER
ASN
21
37
1.47
10
A
A
H
O
PHE
VAL
25
34
1.49
10
A
A
HD22
OG
ASN
SER
11
31
1.54
10
A
A
OD1
HE21
ASN
GLN
11
26
1.54
1
A
ARG
9
0.311
SIDE CHAIN
1
A
ARG
38
0.311
SIDE CHAIN
2
A
ARG
9
0.318
SIDE CHAIN
2
A
ARG
38
0.287
SIDE CHAIN
3
A
ARG
9
0.315
SIDE CHAIN
3
A
ARG
38
0.282
SIDE CHAIN
4
A
ARG
9
0.307
SIDE CHAIN
4
A
ARG
38
0.289
SIDE CHAIN
5
A
ARG
9
0.312
SIDE CHAIN
5
A
ARG
38
0.293
SIDE CHAIN
6
A
ARG
9
0.291
SIDE CHAIN
6
A
ARG
38
0.290
SIDE CHAIN
7
A
ARG
9
0.310
SIDE CHAIN
7
A
ARG
38
0.314
SIDE CHAIN
8
A
ARG
9
0.286
SIDE CHAIN
8
A
ARG
38
0.258
SIDE CHAIN
9
A
ARG
9
0.302
SIDE CHAIN
9
A
ARG
38
0.271
SIDE CHAIN
10
A
ARG
9
0.261
SIDE CHAIN
10
A
ARG
38
0.264
SIDE CHAIN
1
A
PRO
17
-75.91
-78.51
1
A
SER
22
71.13
-4.14
1
A
ASN
37
-76.66
-167.30
2
A
LYS
5
-76.71
-72.94
2
A
SER
21
-98.93
-73.49
2
A
SER
22
-174.33
23.74
3
A
SER
21
-112.90
-75.46
3
A
SER
22
-172.38
14.12
3
A
GLN
30
-151.79
-80.26
3
A
SER
31
174.33
71.66
3
A
ASN
37
-60.60
-76.81
4
A
ASN
6
-97.42
51.37
4
A
ALA
14
-121.16
-71.38
4
A
SER
21
-101.10
-73.36
4
A
SER
22
-168.90
18.65
4
A
ASN
37
-69.34
-83.57
5
A
PRO
17
-74.16
-164.52
5
A
SER
21
-101.11
-75.00
5
A
SER
22
-175.64
18.48
6
A
SER
13
-101.78
44.57
6
A
SER
22
83.68
-3.17
6
A
ASN
37
-55.23
-80.79
7
A
ASN
11
-166.41
-169.91
7
A
SER
22
84.27
-5.04
7
A
ASN
37
-68.40
-89.57
8
A
ALA
14
-129.79
-70.92
8
A
SER
21
-109.90
-75.39
8
A
SER
22
-170.46
25.34
8
A
SER
31
70.61
60.46
9
A
ASN
11
-160.21
-169.91
9
A
SER
21
-107.46
-73.23
9
A
SER
22
-171.17
15.84
9
A
ASN
37
-75.51
-76.01
10
A
ASN
11
-161.19
-141.88
10
A
SER
13
-126.83
-166.52
10
A
PRO
17
-96.49
40.62
10
A
SER
21
-99.28
-72.27
10
A
SER
22
-173.37
13.17
SOLUTION STRUCTURE OF PAFP-S, AN ANTIFUNGAL PEPTIDE FROM THE SEEDS OF PHYTOLACCA AMERICANA
1
N
N
disulf
2.027
A
CYS
3
A
SG
CYS
3
1_555
A
CYS
20
A
SG
CYS
20
1_555
disulf
2.024
A
CYS
10
A
SG
CYS
10
1_555
A
CYS
24
A
SG
CYS
24
1_555
disulf
2.021
A
CYS
19
A
SG
CYS
19
1_555
A
CYS
35
A
SG
CYS
35
1_555
ANTIFUNGAL PROTEIN
THREE-STRANDS BETA SHEET, ANTIFUNGAL PROTEIN
PAFP_PHYAM
UNP
1
P81418
28
65
1DKC
1
38
P81418
A
1
1
38
3
anti-parallel
anti-parallel
A
GLY
8
A
GLY
8
A
CYS
10
A
CYS
10
A
TYR
32
A
TYR
32
A
LYS
36
A
LYS
36
A
TYR
23
A
TYR
23
A
ILE
27
A
ILE
27
1
P 1