1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
RESIDUES PRO 36 AND PRO 42 ARE CIS PROLINES.
Clore, G.M.
Driscoll, P.C.
Gronenborn, A.M.
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
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
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 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 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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
US
Biochemistry
BICHAW
0033
0006-2960
28
2188
2198
10.1021/bi00431a033
2566326
Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.
1989
US
Biochemistry
BICHAW
0033
0006-2960
28
2178
A Proton Nuclear Magnetic Resonance Study of the Antihypertensive and Antiviral Protein Bds-I from the Sea Anemone Anemonia Sulcata. Sequential and Stereospecific Resonance Assignment and Secondary Structure
1989
NE
FEBS Lett.
FEBLAL
0165
0014-5793
243
223
The Influence of Stereospecific Assignments on the Determination of Three-Dimensional Structures of Proteins by Nuclear Magnetic Resonance Spectroscopy. Application to the Sea Anemone Protein Bds-I
1989
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
4719.434
BDS-I
1
man
polymer
no
no
AAPCFCSGKPGRGDLWILRGTCPGGYGYTSNCYKWPNICCYPH
AAPCFCSGKPGRGDLWILRGTCPGGYGYTSNCYKWPNICCYPH
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
n
n
n
n
n
snake-locks sea anemone
Anemonia
sample
6108
Anemonia sulcata
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conf
repository
Initial release
Version format compliance
Version format compliance
Derived calculations
Other
1
0
1989-01-09
1
1
2008-03-24
1
2
2011-07-13
1
3
2017-11-29
_pdbx_database_status.process_site
Y
BNL
1988-11-14
REL
1
REFINEMENT. THE METHOD USED TO DETERMINE AND REFINE THE
STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE
GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD
(M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. 229,
317-324 (1988)) USING THE PROGRAM XPLOR (A.T. BRUENGER,
YALE UNIVERSITY, CT 06511).
STRUCTURAL STATISTICS
RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)*
RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS)
ALL 513 0.079
INTERRESIDUE
SHORT RANGE 150 0.086
INTERRESIDUE
LONG RANGE 105 0.100
INTRARESIDUE 234 0.065
HBOND *(2)* 24 0.043
POTENTIAL ENERGY TERMS
TYPE ENERGY (KCAL/MOL)
F(NOE) *(3)* 160
F(TOR) *(4)* 24
F(REPEL) *(5)* 72
LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED
USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS
-117 KCAL/MOL.
DEVIATIONS FROM IDEALIZED GEOMETRY *(6)*
TYPE TOTAL NUMBER RMS DEVIATION
BONDS 646 0.013 (ANGSTROMS)
ANGLES 1157 2.517 (DEGREES)
IMPROPERS 242 0.797 (DEGREES)
NOTES.
*(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS
ARE CALCULATED WITH RESPECT TO THE UPPER AND
LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF
THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN
0.5 ANGSTROMS.
*(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO
RESTRAINTS - R(NH-O) .LT. 2.3 ANGSTROMS AND
R(N-O) .LT. 3.3 ANGSTROMS. THE LOWER LIMITS
ARE GIVEN BY THE SUM OF THE VAN DER WAALS RADII
OF THE RELEVANT ATOMS.
*(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL
F(NOE) ARE CALCULATED WITH A FORCE CONSTANT OF
50 KCAL/MOL/ANGSTROM**2.
*(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE
CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A
SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO
RESTRICT THE RANGES OF 23 PHI AND 21 CHI1 TORSION
ANGLES, AND THE OMEGA PEPTIDE BOND TORSION ANGLES
OF THE FIVE PROLINE RESIDUES (PRO 36 AND 42 BEING
RESTRAINED TO THE CIS CONFORMATION AND THE OTHERS
TO TRANS).
*(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM
F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF
4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE
VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD
VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY
FUNCTION.
*(6)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY
AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE
PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION
OF PROLINES) IN THE TRANS CONFORMATION. IN THE
DYNAMICAL SIMULATED ANNEALING CALCULATIONS, THE
RESTRAINTS FOR THE DISULFIDE BRIDGES ARE INCLUDED
IN THE BOND AND ANGLE TERMS.
A TOTAL OF 42 STRUCTURES CONSISTENT WITH THE NMR DATA
WERE CALCULATED. THIS ENTRY REPRESENTS THE COORDINATES
OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL
STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO
FURTHER RESTRAINED MINIMIZATION. THE COORDINATES OF THESE
42 STRUCTURES ARE GIVEN IN THE PDB ENTRY *2BDS*.
THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE
ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT
THE MEAN COORDINATE POSITIONS.
ALL THE INTERPROTON DISTANCE AND TORSION ANGLE RESTRAINTS
ARE AVAILABLE IN THE PDB NMR RESTRAINT FILE.
BRUNGER
refinement
XPLOR
ALA
1
n
1
ALA
1
A
ALA
2
n
2
ALA
2
A
PRO
3
n
3
PRO
3
A
CYS
4
n
4
CYS
4
A
PHE
5
n
5
PHE
5
A
CYS
6
n
6
CYS
6
A
SER
7
n
7
SER
7
A
GLY
8
n
8
GLY
8
A
LYS
9
n
9
LYS
9
A
PRO
10
n
10
PRO
10
A
GLY
11
n
11
GLY
11
A
ARG
12
n
12
ARG
12
A
GLY
13
n
13
GLY
13
A
ASP
14
n
14
ASP
14
A
LEU
15
n
15
LEU
15
A
TRP
16
n
16
TRP
16
A
ILE
17
n
17
ILE
17
A
LEU
18
n
18
LEU
18
A
ARG
19
n
19
ARG
19
A
GLY
20
n
20
GLY
20
A
THR
21
n
21
THR
21
A
CYS
22
n
22
CYS
22
A
PRO
23
n
23
PRO
23
A
GLY
24
n
24
GLY
24
A
GLY
25
n
25
GLY
25
A
TYR
26
n
26
TYR
26
A
GLY
27
n
27
GLY
27
A
TYR
28
n
28
TYR
28
A
THR
29
n
29
THR
29
A
SER
30
n
30
SER
30
A
ASN
31
n
31
ASN
31
A
CYS
32
n
32
CYS
32
A
TYR
33
n
33
TYR
33
A
LYS
34
n
34
LYS
34
A
TRP
35
n
35
TRP
35
A
PRO
36
n
36
PRO
36
A
ASN
37
n
37
ASN
37
A
ILE
38
n
38
ILE
38
A
CYS
39
n
39
CYS
39
A
CYS
40
n
40
CYS
40
A
TYR
41
n
41
TYR
41
A
PRO
42
n
42
PRO
42
A
HIS
43
n
43
HIS
43
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
ALA
ALA
1
2
-149.71
1
A
ARG
12
0.305
SIDE CHAIN
1
A
ARG
19
0.200
SIDE CHAIN
1
5.00
0.80
106.30
111.30
A
A
A
CD1
CG
CD2
TRP
TRP
TRP
16
16
16
N
1
-7.25
1.00
110.10
102.85
A
A
A
CG
CD1
NE1
TRP
TRP
TRP
16
16
16
N
1
5.40
0.90
109.00
114.40
A
A
A
CD1
NE1
CE2
TRP
TRP
TRP
16
16
16
N
1
10.13
1.10
130.40
140.53
A
A
A
NE1
CE2
CZ2
TRP
TRP
TRP
16
16
16
N
1
-7.42
1.00
107.30
99.88
A
A
A
NE1
CE2
CD2
TRP
TRP
TRP
16
16
16
N
1
-6.01
0.90
133.90
127.89
A
A
A
CG
CD2
CE3
TRP
TRP
TRP
16
16
16
N
1
-6.35
1.00
110.10
103.75
A
A
A
CG
CD1
NE1
TRP
TRP
TRP
35
35
35
N
1
9.40
1.10
130.40
139.80
A
A
A
NE1
CE2
CZ2
TRP
TRP
TRP
35
35
35
N
1
-7.13
1.00
107.30
100.17
A
A
A
NE1
CE2
CD2
TRP
TRP
TRP
35
35
35
N
1
A
A
CG
CD2
TRP
TRP
16
16
-0.129
0.017
1.432
1.303
N
1
A
A
CG
CD2
TRP
TRP
35
35
-0.114
0.017
1.432
1.318
N
1
A
A
CG
ND1
HIS
HIS
43
43
-0.125
0.015
1.369
1.244
N
1
A
PRO
3
-78.66
20.70
1
A
PRO
10
-67.48
-161.55
1
A
ILE
17
-94.78
-153.52
1
A
LEU
18
-67.72
78.73
1
A
THR
29
-160.53
-38.20
1
A
PRO
36
-78.66
39.10
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
BDS-I (NMR, MINIMIZED MEAN STRUCTURE)
DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE ANTIHYPERTENSIVE AND ANTIVIRAL PROTEIN BDS-I FROM THE SEA ANEMONE ANEMONIA SULCATA. A STUDY USING NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
1
Y
N
disulf
2.017
A
CYS
4
A
SG
CYS
4
1_555
A
CYS
39
A
SG
CYS
39
1_555
disulf
2.026
A
CYS
6
A
SG
CYS
6
1_555
A
CYS
32
A
SG
CYS
32
1_555
disulf
2.023
A
CYS
22
A
SG
CYS
22
1_555
A
CYS
40
A
SG
CYS
40
1_555
ANTI-HYPERTENSIVE, ANTI-VIRAL PROTEIN
ANTI-HYPERTENSIVE, ANTI-VIRAL PROTEIN
A
TRP
35
A
TRP
35
1
A
PRO
36
A
PRO
36
-7.56
A
TYR
41
A
TYR
41
1
A
PRO
42
A
PRO
42
6.48
BDS1_ANESU
UNP
1
1
P11494
AAPCFCSGKPGRGDLWILRGTCPGGYGYTSNCYKWPNICCYPH
1
43
1BDS
1
43
P11494
A
1
1
43
3
anti-parallel
anti-parallel
A
ASP
14
A
ASP
14
A
ILE
17
A
ILE
17
A
ASN
37
A
ASN
37
A
TYR
41
A
TYR
41
A
SER
30
A
SER
30
A
LYS
34
A
LYS
34
1
P 1