1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Skjeldal, L.
Gran, L.
Sletten, K.
Volkman, B.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H13 N O2
131.173
y
LEUCINE
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Arch.Biochem.Biophys.
ABBIA4
0158
0003-9861
399
142
148
10.1006/abbi.2002.2769
11888199
Refined structure and metal binding site of the kalata B1 peptide.
2002
US
Biochemistry
BICHAW
0033
0006-2960
34
4147
4158
Elucidation of the Primary and Three-Dimensional Structure of the Uterotonic Polypeptide Kalata B1
1995
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
2917.345
Kalata-B4
1
nat
polymer
no
no
NGLPVCGETCVGGTCNTPGCTCSWPVCTR
NGLPVCGETCVGGTCNTPGCTCSWPVCTR
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
extracted from plant
Oldenlandia
sample
1
29
60225
Oldenlandia affinis
atom_site
entity
entity_src_nat
pdbx_molecule_features
pdbx_nmr_software
pdbx_poly_seq_scheme
pdbx_struct_assembly
pdbx_struct_oper_list
pdbx_validate_close_contact
pdbx_validate_torsion
struct_conn
struct_mon_prot_cis
struct_ref
struct_ref_seq
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Advisory
Atomic model
Data collection
Database references
Derived calculations
Source and taxonomy
Structure summary
1
0
2002-06-12
1
1
2008-04-27
1
2
2011-07-13
2
0
2020-08-12
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.auth_seq_id
_atom_site.label_atom_id
_entity.pdbx_description
_entity_src_nat.pdbx_beg_seq_num
_entity_src_nat.pdbx_end_seq_num
_pdbx_nmr_software.name
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_validate_close_contact.auth_atom_id_1
_pdbx_validate_close_contact.auth_seq_id_1
_pdbx_validate_close_contact.auth_seq_id_2
_pdbx_validate_torsion.auth_seq_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_seq_id
_struct_mon_prot_cis.auth_seq_id
_struct_mon_prot_cis.pdbx_auth_seq_id_2
_struct_ref.db_code
_struct_ref.pdbx_db_accession
_struct_ref.pdbx_seq_one_letter_code
ELUCIDATION OF THE PRIMARY AND THREE-DIMENSIONAL STRUCTURE OF THE UTEROTONIC POLYPEPTIDE KALATA B1
RCSB
Y
RCSB
2001-07-10
REL
REL
Antimicrobial, Antitumor
KALATA B1
Cyclic peptide
Structure was determined using NOEs from a single 100 ms mixing time NOESY experiment
target function
50
20
2D NOESY
0
3
ambient
298
K
Structures are based on a total of 333 distance constraints. This includes 6 upper and 6 lower limits defining 3 disulfide bonds, as well as 3 upper and 3 lower limits defining a peptide bond cyclizing the peptide backbone.
Residue numbering follows the original description of citation 1, except that for the purposes of structure calculations, the N-terminal residue was taken as Asn8. Therefore, residues 30-36 in this deposition correspond to residues 1-7 in citation 1 and related PDB entry 1kal.
Structures were refined in the absence of any artificial constraints defining disulfide bonds until all NOEs had been assigned and low target functions were achieved (tf=0.6). 15 additional calculations were performed with these input data and the inclusion of constraints defining all possible disulfide pairing combinations. The structures containing disulfides between [5(34)-13], [17-29] and [22-27] displayed the lowest target function (0.74, second lowest was 1.54). On the basis of this result and analysis of NOEs observed between Cys sidechain protons, this disulfide bonding arrangement was assumed to be correct and served as the basis for this deposition.
torsion angle dynamics
5 mM kalata B1; 90% H2O, 10% D2O
90% H2O/10% D2O
P. Guentert
refinement
DYANA
1.5
Bruker
collection
XwinNMR
2.6
C. Bartels
data analysis
XEASY
1.3.11
750
Bruker
DMX
ASN
8
n
1
ASN
1
A
GLY
9
n
2
GLY
2
A
LEU
10
n
3
LEU
3
A
PRO
11
n
4
PRO
4
A
VAL
12
n
5
VAL
5
A
CYS
13
n
6
CYS
6
A
GLY
14
n
7
GLY
7
A
GLU
15
n
8
GLU
8
A
THR
16
n
9
THR
9
A
CYS
17
n
10
CYS
10
A
VAL
18
n
11
VAL
11
A
GLY
19
n
12
GLY
12
A
GLY
20
n
13
GLY
13
A
THR
21
n
14
THR
14
A
CYS
22
n
15
CYS
15
A
ASN
23
n
16
ASN
16
A
THR
24
n
17
THR
17
A
PRO
25
n
18
PRO
18
A
GLY
26
n
19
GLY
19
A
CYS
27
n
20
CYS
20
A
THR
28
n
21
THR
21
A
CYS
29
n
22
CYS
22
A
SER
30
n
23
SER
23
A
TRP
31
n
24
TRP
24
A
PRO
32
n
25
PRO
25
A
VAL
33
n
26
VAL
26
A
CYS
34
n
27
CYS
27
A
THR
35
n
28
THR
28
A
ARG
36
n
29
ARG
29
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
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
A
N
C
ASN
ARG
1
29
1.37
2
A
A
N
C
ASN
ARG
1
29
1.37
3
A
A
H1
C
ASN
ARG
1
29
1.36
3
A
A
N
C
ASN
ARG
1
29
1.37
4
A
A
N
C
ASN
ARG
1
29
1.37
5
A
A
N
C
ASN
ARG
1
29
1.38
6
A
A
N
C
ASN
ARG
1
29
1.37
7
A
A
N
C
ASN
ARG
1
29
1.37
8
A
A
N
C
ASN
ARG
1
29
1.38
8
A
A
H
O
THR
THR
21
28
1.59
9
A
A
N
C
ASN
ARG
1
29
1.38
10
A
A
N
C
ASN
ARG
1
29
1.38
10
A
A
H1
C
ASN
ARG
1
29
1.48
11
A
A
N
C
ASN
ARG
1
29
1.37
12
A
A
N
C
ASN
ARG
1
29
1.38
13
A
A
N
C
ASN
ARG
1
29
1.37
14
A
A
N
C
ASN
ARG
1
29
1.38
15
A
A
H1
C
ASN
ARG
1
29
0.75
15
A
A
H1
O
ASN
ARG
1
29
1.29
15
A
A
N
C
ASN
ARG
1
29
1.31
16
A
A
N
C
ASN
ARG
1
29
1.38
16
A
A
O
H
LEU
ARG
3
29
1.59
17
A
A
N
C
ASN
ARG
1
29
1.36
18
A
A
N
C
ASN
ARG
1
29
1.38
19
A
A
N
C
ASN
ARG
1
29
1.36
20
A
A
N
C
ASN
ARG
1
29
1.37
1
A
CYS
10
-154.46
68.76
1
A
ASN
16
59.86
16.01
1
A
CYS
22
-38.81
114.56
1
A
TRP
24
62.46
137.26
2
A
CYS
10
-153.93
65.90
2
A
ASN
16
82.43
-1.05
2
A
CYS
22
-39.93
109.78
2
A
TRP
24
62.73
137.62
3
A
VAL
5
-142.24
22.82
3
A
CYS
10
-153.36
66.70
3
A
CYS
22
-38.26
113.32
3
A
TRP
24
62.37
136.22
4
A
LEU
3
-52.54
109.41
4
A
CYS
10
-155.54
62.86
4
A
CYS
22
-36.68
112.37
4
A
TRP
24
62.59
136.72
5
A
VAL
5
-142.39
23.52
5
A
CYS
10
-154.28
66.07
5
A
ASN
16
84.33
-0.93
5
A
CYS
22
-38.29
114.43
5
A
TRP
24
62.22
135.97
6
A
ASN
16
82.53
-0.93
6
A
TRP
24
61.87
138.69
7
A
VAL
5
-143.79
20.77
7
A
CYS
10
-153.13
68.91
7
A
ASN
16
79.26
-0.98
7
A
TRP
24
62.16
135.61
8
A
CYS
10
-155.93
71.57
8
A
CYS
22
-39.59
118.94
8
A
TRP
24
62.32
135.27
9
A
CYS
10
-152.28
71.63
9
A
ASN
16
79.57
-1.20
9
A
CYS
22
-37.51
112.53
9
A
TRP
24
62.58
136.71
10
A
CYS
10
-152.50
74.80
10
A
ASN
16
83.27
-1.80
10
A
CYS
22
-38.86
114.85
10
A
TRP
24
62.65
135.94
11
A
VAL
5
-145.10
22.42
11
A
CYS
10
-154.59
68.75
11
A
CYS
22
-39.05
113.98
11
A
TRP
24
62.42
134.26
12
A
CYS
10
-155.18
72.58
12
A
TRP
24
62.33
135.45
13
A
VAL
5
-140.77
24.92
13
A
CYS
10
-154.58
71.86
13
A
CYS
22
-38.55
118.88
13
A
TRP
24
62.43
134.99
14
A
VAL
5
-147.84
23.64
14
A
CYS
10
-151.81
73.46
14
A
ASN
16
80.72
-1.36
14
A
CYS
22
-38.55
113.35
14
A
TRP
24
62.49
136.38
15
A
VAL
5
-144.25
17.19
15
A
CYS
10
-156.69
69.16
15
A
CYS
22
-24.05
116.55
15
A
TRP
24
62.54
137.45
16
A
LEU
3
-57.45
109.54
16
A
CYS
10
-152.20
74.15
16
A
ASN
16
79.61
-1.70
16
A
THR
21
-119.74
70.47
16
A
CYS
22
-34.50
117.20
16
A
TRP
24
62.73
137.02
17
A
CYS
10
-151.78
67.43
17
A
CYS
22
-38.49
112.82
17
A
TRP
24
62.35
136.28
18
A
CYS
10
-153.89
72.33
18
A
CYS
15
-47.84
165.29
18
A
TRP
24
62.14
135.74
19
A
CYS
10
-155.94
72.08
19
A
CYS
22
-28.56
119.50
19
A
TRP
24
62.43
136.67
20
A
CYS
10
-150.13
60.53
20
A
CYS
22
-26.09
117.36
20
A
TRP
24
62.53
138.01
KALATA B1
REFINED STRUCTURE AND DISULFIDE PAIRING OF THE KALATA B1 PEPTIDE
1
N
N
disulf
1.978
A
CYS
6
A
SG
CYS
6
1_555
A
CYS
27
A
SG
CYS
27
1_555
disulf
2.105
A
CYS
10
A
SG
CYS
10
1_555
A
CYS
22
A
SG
CYS
22
1_555
disulf
1.996
A
CYS
15
A
SG
CYS
15
1_555
A
CYS
20
A
SG
CYS
20
1_555
PLANT PROTEIN
cyclic peptide, cyclotide, disulfide pairing, uterotonic, PLANT PROTEIN
A
TRP
24
A
TRP
24
1
A
PRO
25
A
PRO
25
-0.02
A
TRP
24
A
TRP
24
2
A
PRO
25
A
PRO
25
0.02
A
TRP
24
A
TRP
24
3
A
PRO
25
A
PRO
25
-0.05
A
TRP
24
A
TRP
24
4
A
PRO
25
A
PRO
25
-0.04
A
TRP
24
A
TRP
24
5
A
PRO
25
A
PRO
25
0.05
A
TRP
24
A
TRP
24
6
A
PRO
25
A
PRO
25
-0.01
A
TRP
24
A
TRP
24
7
A
PRO
25
A
PRO
25
-0.04
A
TRP
24
A
TRP
24
8
A
PRO
25
A
PRO
25
0.01
A
TRP
24
A
TRP
24
9
A
PRO
25
A
PRO
25
0.05
A
TRP
24
A
TRP
24
10
A
PRO
25
A
PRO
25
0.00
A
TRP
24
A
TRP
24
11
A
PRO
25
A
PRO
25
0.07
A
TRP
24
A
TRP
24
12
A
PRO
25
A
PRO
25
-0.10
A
TRP
24
A
TRP
24
13
A
PRO
25
A
PRO
25
0.02
A
TRP
24
A
TRP
24
14
A
PRO
25
A
PRO
25
0.06
A
TRP
24
A
TRP
24
15
A
PRO
25
A
PRO
25
0.02
A
TRP
24
A
TRP
24
16
A
PRO
25
A
PRO
25
0.01
A
TRP
24
A
TRP
24
17
A
PRO
25
A
PRO
25
0.06
A
TRP
24
A
TRP
24
18
A
PRO
25
A
PRO
25
-0.01
A
TRP
24
A
TRP
24
19
A
PRO
25
A
PRO
25
-0.07
A
TRP
24
A
TRP
24
20
A
PRO
25
A
PRO
25
0.03
KAB4_OLDAF
UNP
1
1
P83938
GLPVCGETCVGGTCNTPGCTCSWPVCTR
1
28
1JJZ
2
29
P83938
A
1
2
29
1
expression tag
ASN
1
1JJZ
A
P83938
UNP
1