1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Mandard, N.
Bulet, P.
Caille, A.
Daffre, S.
Vovelle, F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C6 H15 N4 O2 1
175.209
y
ARGININE
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
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
H2 N
16.023
AMINO GROUP
non-polymer
C5 H7 N O3
129.114
n
PYROGLUTAMIC ACID
L-peptide linking
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
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
269
1190
1198
10.1046/j.0014-2956.2002.02760.x
11856345
The solution structure of gomesin, an antimicrobial cysteine-rich peptide from the spider.
2002
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
275
33464
33470
10.1074/jbc.M001491200
Isolation and characterization of gomesin, an 18-residue cysteine-rich defense peptide from the spider Acanthoscurria gomesiana hemocytes with sequence similarities to horseshoe crab antimicrobial peptides of the tachyplesin family
2000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
2279.762
GOMESIN
1
syn
polymer
no
yes
(PCA)CRRLCYKQRCVTYCRGR(NH2)
QCRRLCYKQRCVTYCRGRX
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
entity_poly
pdbx_entity_src_syn
pdbx_struct_assembly
pdbx_struct_mod_residue
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Polymer sequence
Source and taxonomy
1
0
2002-04-10
1
1
2008-04-27
1
2
2011-07-13
2
0
2019-12-25
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_entity_src_syn.details
_pdbx_entity_src_syn.ncbi_taxonomy_id
_pdbx_entity_src_syn.organism_common_name
_pdbx_entity_src_syn.organism_scientific
_pdbx_struct_mod_residue.parent_comp_id
_struct_conn.pdbx_leaving_atom_flag
RCSB
Y
PDBJ
2001-11-22
REL
115339
mygalomorphae spider
Acanthoscurria gomesiana
sample
This solution structure was determined using standard 2D homonuclear techniques.
structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
200
20
DQF-COSY
2D NOESY
clean-TOCSY
2D NOESY
Clean-TOCSY
2D NOESY
Clean-TOCSY
3.5
ambient
278
K
3.5
ambient
285
K
The 20 structures are based on a total of 289 restraints, 279 are NOE-derived distance constraints, 4 are used for hydrogen bonds modelling and 6 (i.e. 2x3) are used for disulfide bridge modelling.
No dihedral angle restraints used.
distance geometry
simulated annealing
energy minimization
3.3mM Gomesin
90% H2O/10% D2O
3.3mM Gomesin
100% D2O
Guentert
structure solution
DYANA
1.5
Brunger
refinement
X-PLOR
3.1
Varian, Inc.
processing
VNMR
6.1
600
Varian
INOVA
PCA
1
n
1
PCA
1
A
CYS
2
n
2
CYS
2
A
ARG
3
n
3
ARG
3
A
ARG
4
n
4
ARG
4
A
LEU
5
n
5
LEU
5
A
CYS
6
n
6
CYS
6
A
TYR
7
n
7
TYR
7
A
LYS
8
n
8
LYS
8
A
GLN
9
n
9
GLN
9
A
ARG
10
n
10
ARG
10
A
CYS
11
n
11
CYS
11
A
VAL
12
n
12
VAL
12
A
THR
13
n
13
THR
13
A
TYR
14
n
14
TYR
14
A
CYS
15
n
15
CYS
15
A
ARG
16
n
16
ARG
16
A
GLY
17
n
17
GLY
17
A
ARG
18
n
18
ARG
18
A
NH2
19
n
19
NH2
19
A
author_defined_assembly
1
monomeric
A
PCA
1
PYROGLUTAMIC ACID
A
PCA
1
GLN
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
5
A
N
LEU
5
A
O
VAL
12
A
O
VAL
12
1
A
ARG
3
0.233
SIDE CHAIN
1
A
ARG
4
0.314
SIDE CHAIN
1
A
ARG
10
0.317
SIDE CHAIN
1
A
ARG
16
0.311
SIDE CHAIN
1
A
ARG
18
0.301
SIDE CHAIN
2
A
ARG
3
0.301
SIDE CHAIN
2
A
ARG
4
0.279
SIDE CHAIN
2
A
ARG
10
0.314
SIDE CHAIN
2
A
ARG
16
0.302
SIDE CHAIN
2
A
ARG
18
0.156
SIDE CHAIN
3
A
ARG
3
0.305
SIDE CHAIN
3
A
ARG
4
0.286
SIDE CHAIN
3
A
ARG
10
0.308
SIDE CHAIN
3
A
ARG
16
0.239
SIDE CHAIN
3
A
ARG
18
0.317
SIDE CHAIN
4
A
ARG
3
0.308
SIDE CHAIN
4
A
ARG
4
0.292
SIDE CHAIN
4
A
ARG
10
0.308
SIDE CHAIN
4
A
ARG
16
0.322
SIDE CHAIN
4
A
ARG
18
0.318
SIDE CHAIN
5
A
ARG
3
0.269
SIDE CHAIN
5
A
ARG
4
0.313
SIDE CHAIN
5
A
ARG
10
0.107
SIDE CHAIN
5
A
ARG
16
0.309
SIDE CHAIN
5
A
ARG
18
0.317
SIDE CHAIN
6
A
ARG
3
0.331
SIDE CHAIN
6
A
ARG
4
0.304
SIDE CHAIN
6
A
ARG
10
0.283
SIDE CHAIN
6
A
ARG
16
0.253
SIDE CHAIN
6
A
ARG
18
0.305
SIDE CHAIN
7
A
ARG
3
0.301
SIDE CHAIN
7
A
ARG
4
0.304
SIDE CHAIN
7
A
ARG
10
0.208
SIDE CHAIN
7
A
ARG
16
0.269
SIDE CHAIN
7
A
ARG
18
0.305
SIDE CHAIN
8
A
ARG
3
0.122
SIDE CHAIN
8
A
ARG
4
0.293
SIDE CHAIN
8
A
ARG
10
0.205
SIDE CHAIN
8
A
ARG
16
0.314
SIDE CHAIN
8
A
ARG
18
0.302
SIDE CHAIN
9
A
ARG
3
0.206
SIDE CHAIN
9
A
ARG
4
0.313
SIDE CHAIN
9
A
ARG
16
0.237
SIDE CHAIN
9
A
ARG
18
0.295
SIDE CHAIN
10
A
ARG
3
0.249
SIDE CHAIN
10
A
ARG
4
0.312
SIDE CHAIN
10
A
ARG
10
0.320
SIDE CHAIN
10
A
ARG
16
0.322
SIDE CHAIN
10
A
ARG
18
0.279
SIDE CHAIN
11
A
ARG
3
0.284
SIDE CHAIN
11
A
ARG
4
0.312
SIDE CHAIN
11
A
ARG
10
0.303
SIDE CHAIN
11
A
ARG
16
0.306
SIDE CHAIN
11
A
ARG
18
0.309
SIDE CHAIN
12
A
ARG
3
0.136
SIDE CHAIN
12
A
ARG
4
0.278
SIDE CHAIN
12
A
ARG
10
0.313
SIDE CHAIN
12
A
ARG
16
0.312
SIDE CHAIN
12
A
ARG
18
0.315
SIDE CHAIN
13
A
ARG
3
0.088
SIDE CHAIN
13
A
ARG
4
0.294
SIDE CHAIN
13
A
ARG
10
0.316
SIDE CHAIN
13
A
ARG
16
0.165
SIDE CHAIN
13
A
ARG
18
0.312
SIDE CHAIN
14
A
ARG
3
0.281
SIDE CHAIN
14
A
ARG
4
0.314
SIDE CHAIN
14
A
ARG
10
0.309
SIDE CHAIN
14
A
ARG
16
0.287
SIDE CHAIN
14
A
ARG
18
0.310
SIDE CHAIN
15
A
ARG
3
0.328
SIDE CHAIN
15
A
ARG
4
0.298
SIDE CHAIN
15
A
ARG
10
0.295
SIDE CHAIN
15
A
ARG
16
0.316
SIDE CHAIN
15
A
ARG
18
0.321
SIDE CHAIN
16
A
ARG
3
0.316
SIDE CHAIN
16
A
ARG
4
0.300
SIDE CHAIN
16
A
ARG
10
0.304
SIDE CHAIN
16
A
ARG
16
0.311
SIDE CHAIN
16
A
ARG
18
0.309
SIDE CHAIN
17
A
ARG
3
0.321
SIDE CHAIN
17
A
ARG
4
0.282
SIDE CHAIN
17
A
ARG
10
0.159
SIDE CHAIN
17
A
ARG
16
0.317
SIDE CHAIN
17
A
ARG
18
0.309
SIDE CHAIN
18
A
ARG
3
0.075
SIDE CHAIN
18
A
ARG
4
0.309
SIDE CHAIN
18
A
ARG
10
0.291
SIDE CHAIN
18
A
ARG
16
0.314
SIDE CHAIN
18
A
ARG
18
0.310
SIDE CHAIN
19
A
ARG
3
0.312
SIDE CHAIN
19
A
ARG
4
0.266
SIDE CHAIN
19
A
ARG
10
0.141
SIDE CHAIN
19
A
ARG
16
0.189
SIDE CHAIN
19
A
ARG
18
0.312
SIDE CHAIN
20
A
ARG
3
0.322
SIDE CHAIN
20
A
ARG
4
0.290
SIDE CHAIN
20
A
ARG
10
0.312
SIDE CHAIN
20
A
ARG
16
0.311
SIDE CHAIN
20
A
ARG
18
0.316
SIDE CHAIN
2
-6.19
0.50
120.30
114.11
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
3
3
3
N
2
6.95
1.10
119.40
126.35
A
A
A
NH1
CZ
NH2
ARG
ARG
ARG
4
4
4
N
2
-4.87
0.50
120.30
115.43
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
2
-4.32
0.50
120.30
115.98
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
10
10
10
N
2
-3.39
0.50
120.30
116.91
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
3
-5.56
0.50
120.30
114.74
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
3
3
3
N
3
6.69
1.10
119.40
126.09
A
A
A
NH1
CZ
NH2
ARG
ARG
ARG
4
4
4
N
3
-4.74
0.50
120.30
115.56
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
3
-4.43
0.60
121.00
116.57
A
A
A
CB
CG
CD2
TYR
TYR
TYR
7
7
7
N
3
4.16
0.60
121.00
125.16
A
A
A
CB
CG
CD1
TYR
TYR
TYR
7
7
7
N
3
-4.73
0.50
120.30
115.57
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
10
10
10
N
3
4.06
0.60
121.00
125.06
A
A
A
CB
CG
CD1
TYR
TYR
TYR
14
14
14
N
3
-3.59
0.50
120.30
116.71
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
4
-3.96
0.50
120.30
116.34
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
4
-4.01
0.50
120.30
116.29
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
5
-5.35
0.50
120.30
114.95
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
3
3
3
N
6
-3.63
0.50
120.30
116.67
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
6
-4.03
0.50
120.30
116.27
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
6
-4.66
0.50
120.30
115.64
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
10
10
10
N
6
-3.50
0.50
120.30
116.80
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
6
-3.34
0.50
120.30
116.96
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
18
18
18
N
7
-4.01
0.50
120.30
116.29
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
7
-3.27
0.50
120.30
117.03
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
18
18
18
N
8
-4.36
0.50
120.30
115.94
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
8
-4.52
0.50
120.30
115.78
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
10
10
10
N
9
-3.11
0.50
120.30
117.19
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
9
-3.44
0.50
120.30
116.86
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
9
-3.83
0.50
120.30
116.47
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
9
-3.31
0.50
120.30
116.99
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
18
18
18
N
10
-4.17
0.50
120.30
116.13
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
10
-3.70
0.50
120.30
116.60
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
10
-3.51
0.50
120.30
116.79
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
11
-3.24
0.50
120.30
117.06
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
11
-3.24
0.50
120.30
117.06
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
11
-3.41
0.50
120.30
116.89
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
18
18
18
N
12
-4.22
0.50
120.30
116.08
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
13
-3.38
0.50
120.30
116.92
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
4
4
4
N
13
-4.16
0.50
120.30
116.14
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
10
10
10
N
13
-3.34
0.50
120.30
116.96
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
18
18
18
N
14
-4.52
0.50
120.30
115.78
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
14
-3.06
0.50
120.30
117.24
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
18
18
18
N
15
-4.67
0.50
120.30
115.63
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
15
-3.32
0.50
120.30
116.98
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
15
-3.08
0.50
120.30
117.22
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
18
18
18
N
16
-3.22
0.50
120.30
117.08
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
16
-4.67
0.50
120.30
115.63
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
16
-3.30
0.50
120.30
117.00
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
10
10
10
N
16
-3.20
0.50
120.30
117.10
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
17
7.16
1.10
114.20
121.36
A
A
A
CA
CB
SG
CYS
CYS
CYS
2
2
2
N
17
-3.21
0.50
120.30
117.09
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
17
-3.03
0.50
120.30
117.27
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
16
16
16
N
17
-3.01
0.50
120.30
117.29
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
18
18
18
N
18
-3.13
0.50
120.30
117.17
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
3
3
3
N
18
-3.49
0.50
120.30
116.81
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
18
-3.81
0.50
120.30
116.49
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
10
10
10
N
18
-3.05
0.50
120.30
117.25
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
18
18
18
N
19
-3.94
0.50
120.30
116.36
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
4
4
4
N
20
-3.76
0.50
120.30
116.54
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
3
3
3
N
20
-3.32
0.50
120.30
116.98
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
20
-3.44
0.50
120.30
116.86
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
10
10
10
N
20
-3.13
0.50
120.30
117.17
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
16
16
16
N
1
A
LYS
8
25.14
25.59
1
A
GLN
9
-175.34
-47.03
2
A
LYS
8
39.93
18.82
2
A
GLN
9
-170.27
-47.65
3
A
TYR
7
-102.15
57.40
3
A
LYS
8
67.98
-47.45
4
A
LYS
8
41.03
11.24
4
A
GLN
9
-158.35
-51.97
5
A
LYS
8
36.87
13.98
5
A
GLN
9
-157.07
-53.73
6
A
TYR
7
-101.91
78.32
6
A
LYS
8
18.68
34.98
6
A
GLN
9
178.04
-40.10
7
A
TYR
7
-102.98
79.24
7
A
LYS
8
16.41
40.52
7
A
GLN
9
172.19
-39.32
8
A
LYS
8
39.54
9.77
8
A
GLN
9
-144.81
-52.84
9
A
LYS
8
43.29
14.57
9
A
GLN
9
-161.58
-55.49
10
A
TYR
7
-101.30
65.28
10
A
LYS
8
38.68
12.85
10
A
GLN
9
-149.59
-51.83
11
A
LYS
8
21.99
73.76
11
A
GLN
9
129.05
-55.12
12
A
TYR
7
-106.78
61.76
12
A
LYS
8
30.43
42.75
12
A
GLN
9
-176.64
-64.12
13
A
TYR
7
-101.06
74.47
13
A
LYS
8
41.81
23.62
13
A
GLN
9
-173.77
-50.62
14
A
LYS
8
0.72
76.88
14
A
GLN
9
148.62
-46.87
15
A
LYS
8
37.66
7.58
15
A
GLN
9
-157.30
-45.98
16
A
LYS
8
68.10
-67.66
16
A
GLN
9
-141.49
-10.28
17
A
LYS
8
17.50
44.73
17
A
GLN
9
170.55
-53.06
18
A
LYS
8
35.11
13.92
18
A
GLN
9
-168.38
-47.53
19
A
LYS
8
32.04
51.03
19
A
GLN
9
169.81
-62.55
20
A
LYS
8
69.25
-62.22
GOMESIN
Solution structure of the antimicrobial 18-residue gomesin
1
N
N
disulf
2.022
A
CYS
2
A
SG
CYS
2
1_555
A
CYS
15
A
SG
CYS
15
1_555
disulf
2.024
A
CYS
6
A
SG
CYS
6
1_555
A
CYS
11
A
SG
CYS
11
1_555
covale
1.286
both
A
PCA
1
A
C
PCA
1
1_555
A
CYS
2
A
N
CYS
2
1_555
covale
1.298
both
A
ARG
18
A
C
ARG
18
1_555
A
NH2
19
A
N
NH2
19
1_555
ANTIBIOTIC
hairpin-like, beta-sheet, disulfide bridges, ANTIBIOTIC
GOME_ACAGO
UNP
1
1
P82358
QCRRLCYKQRCVTYCRGR
1
18
1KFP
1
18
P82358
A
1
1
18
2
anti-parallel
A
CYS
2
A
CYS
2
A
TYR
7
A
TYR
7
A
ARG
10
A
ARG
10
A
CYS
15
A
CYS
15
BINDING SITE FOR RESIDUE NH2 A 19
Software
1
A
ARG
18
A
ARG
18
1
1_555