1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Sticht, H.
Ejchart, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C3 H7 N O2
89.093
y
ALANINE
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
C5 H10 N2 O3
146.144
y
GLUTAMINE
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
ISOLEUCINE
L-peptide linking
La 3
138.905
LANTHANUM (III) ION
non-polymer
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
H2 N
16.023
AMINO GROUP
non-polymer
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
96
903
908
10.1073/pnas.96.3.903
9927666
Alpha-helix nucleation by a calcium-binding peptide loop.
1999
10.2210/pdb1nkf/pdb
pdb_00001nkf
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
LA3+ ION BOUND
1606.649
CALCIUM-BINDING HEXADECAPEPTIDE
D5N
1
man
polymer
138.905
LANTHANUM (III) ION
1
syn
non-polymer
CALMODULIN
no
yes
(ACE)DKDGDGYISAAEAAAQ(NH2)
XDKDGDGYISAAEAAAQX
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
sample
9606
Homo sapiens
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1999-02-16
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1998-03-09
REL
REL
LA
LANTHANUM (III) ION
ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
100
30
NOESY
TOCSY
COSY
1H-13C-HMQC
120mM
6.0
10E+5 PA
atm
275.2
K
DESCRIPTION OF THE STRATEGY USED FOR NMR STRUCTURE CALCULATION AND REFINEMENT: NOE CROSS-PEAKS WERE DIVIDED INTO THREE CATEGORIES AND ASSIGNED DISTANCE RANGES ACCORDING TO THEIR INTENSITY: STRONG, 0.18 - 0.27 NM; MEDIUM, 0.18 - 0.40 NM; WEAK, 0.18 - 0.55 NM. PEAK INTENSITIES WERE ESTIMATED FROM THE NUMBER OF CONTOURS IN NOESY SPECTRUM. HARMONIC RESTRAINTS FOR THE LA3+-ION WERE DEDUCED FROM THE POSITION OF THE CORRESPONDING CA2+-ION CRYSTAL STRUCTURE OF CALMODULIN (PDB CODE: 1CDM). A TOTAL OF SIX HARMONIC DISTANCE RESTRAINTS WAS INCLUDED IN ORDER TO FIX THE DISTANCE AND THE OCTAHEDRAL ARRANGEMENT OF THE SIX LIGANDS RELATIVE TO THE LA3+-ION ASSUMING THE SAME COORDINATION AS FOR THE CA2+ ION IN THE CALMODULIN CRYSTAL STRUCTURE. THE STRUCTURE CALCULATIONS USED THE AB INITIO SIMULATED ANNEALING (SA.INP) AND REFINEMENT (REFINE.INP) PROTOCOLS FROM THE X-PLOR PROGRAM PACKAGE. THE CALCULATIONS STARTED FROM AN EXTENDED TEMPLATE WITH RANDOMIZED BACKBONE TORSION ANGLES FOLLOWED BY 50 CYCLES OF ENERGY MINIMIZATION TO REMOVE CLOSE NON-BONDED CONTACTS. THE HIGH TEMPERATURE PHASE COMPRISED 50 PS OF DYNAMICS AT 1000 K; THE FINAL 16 PS HAD AN INCREASED WEIGHT ON COVALENT GEOMETRY RESTRAINTS AND THE NOE DERIVED DISTANCE RESTRAINTS. IN THE NEXT PHASE THE SYSTEM WAS SLOWLY COOLED FROM 1000 K TO 100 K IN A TIME OF 30 PS FOLLOWED BY 200 STEPS OF ENERGY MINIMIZATION. FOR THE NOE EFFECTIVE ENERGY TERM, REPRESENTING THE INTERPROTON DISTANCES, A SOFT SQUARE-WELL POTENTIAL WAS APPLIED. THE REFINEMENT PROTOCOL CONSISTED OF A SLOW-COOLING FROM 1000 TO 100 K WITHIN 45 PS. A FORCE CONSTANT OF 200 KCAL MOL-1 RAD-1 WAS USED FOR THE DIHEDRAL ANGLE RESTRAINTS WHILE THE NOE DERIVED DISTANCE RESTRAINTS AND HARMONIC RESTRAINT WERE REPRESENTED BY A SQUARE-WELL POTENTIAL FUNCTION WITH FORCE CONSTANT OF 50 KCAL/MOL1/A2. OF THE 200 RESULTING STRUCTURES, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST ENERGY AND THE LEAST VIOLATION OF THE EXPERIMENTAL DATA WERE SELECTED FOR FURTHER CHARACTERIZATION. GEOMETRY OF THE STRUCTURES AND ELEMENTS OF SECONDARY STRUCTURE WERE ANALYZED USING PROCHECK AND DSSP.
SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
1
H2O/D2O(9:1)
BRUNGER
refinement
X-PLOR
structure solution
NDEE
structure solution
X-PLOR
600
Bruker
AMX600
LA
18
2
LA
LA
18
A
ACE
0
n
1
ACE
0
A
ASP
1
n
2
ASP
1
A
LYS
2
n
3
LYS
2
A
ASP
3
n
4
ASP
3
A
GLY
4
n
5
GLY
4
A
ASP
5
n
6
ASP
5
A
GLY
6
n
7
GLY
6
A
TYR
7
n
8
TYR
7
A
ILE
8
n
9
ILE
8
A
SER
9
n
10
SER
9
A
ALA
10
n
11
ALA
10
A
ALA
11
n
12
ALA
11
A
GLU
12
n
13
GLU
12
A
ALA
13
n
14
ALA
13
A
ALA
14
n
15
ALA
14
A
ALA
15
n
16
ALA
15
A
GLN
16
n
17
GLN
16
A
NH2
17
n
18
NH2
17
A
author_defined_assembly
1
monomeric
A
ASP
5
A
OD1
ASP
6
1_555
A
LA
18
B
LA
LA
1_555
A
GLU
12
A
OE2
GLU
13
1_555
152.3
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
H
GLU
ALA
12
15
1.60
3
A
A
OD2
H
ASP
GLY
1
6
1.48
4
A
A
OD2
H
ASP
GLY
1
6
1.59
6
A
A
O
H
SER
ALA
9
13
1.59
11
A
A
O
H
SER
ALA
9
13
1.59
13
A
A
O
HN2
ALA
NH2
13
17
1.49
13
A
A
O
HE21
GLU
GLN
12
16
1.58
14
A
A
O
H
SER
ALA
9
13
1.56
14
A
A
H
OE1
SER
GLU
9
12
1.59
16
A
A
O
H
SER
ALA
9
13
1.58
16
A
A
H
OE1
SER
GLU
9
12
1.59
17
A
A
H
OE1
SER
GLU
9
12
1.59
19
A
A
O
H
SER
ALA
9
13
1.52
20
A
A
H
OE1
SER
GLU
9
12
1.57
21
A
A
H
OE1
SER
GLU
9
12
1.55
22
A
A
H
OE1
SER
GLU
9
12
1.56
22
A
A
O
H
SER
ALA
9
13
1.57
23
A
A
H
OE1
SER
GLU
9
12
1.54
23
A
A
O
H
SER
ALA
9
13
1.55
24
A
A
O
H
SER
ALA
9
13
1.56
25
A
A
H
OE1
SER
GLU
9
12
1.55
25
A
A
O
H
SER
ALA
9
13
1.57
28
A
A
O
H
SER
ALA
9
13
1.54
29
A
A
O
H
SER
ALA
9
13
1.54
29
A
A
H
OE1
SER
GLU
9
12
1.57
30
A
A
OD2
H
ASP
GLY
1
6
1.45
30
A
A
OD2
H
ASP
ASP
1
5
1.55
1
A
ALA
10
-54.97
-75.94
3
A
ALA
10
-61.49
-73.01
5
A
ALA
10
-62.80
-71.80
7
A
ALA
10
-65.02
-73.89
8
A
ALA
10
-63.87
-70.76
10
A
ALA
10
-65.42
-73.34
11
A
ALA
10
-60.72
-74.50
12
A
ASP
3
-137.50
-44.53
13
A
ALA
10
-58.91
-72.63
14
A
ALA
10
-59.34
-76.06
16
A
ALA
10
-55.53
-72.81
17
A
ALA
10
-60.93
-71.48
20
A
ALA
10
-63.61
-74.54
22
A
ALA
10
-52.01
-73.94
23
A
ALA
10
-57.59
-74.80
24
A
ALA
10
-45.26
-71.98
26
A
ALA
10
-62.91
-75.65
27
A
ALA
10
-63.79
-72.24
28
A
ASP
3
-104.39
-63.64
28
A
ALA
10
-44.98
-70.92
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
CALCIUM-BINDING PEPTIDE, NMR, 30 STRUCTURES
1
Y
N
2
N
N
A
ALA
10
A
ALA
11
HELX_P
A
ALA
14
A
ALA
15
1
1
5
covale
1.305
both
A
ACE
0
A
C
ACE
1
1_555
A
ASP
1
A
N
ASP
2
1_555
covale
1.305
both
A
GLN
16
A
C
GLN
17
1_555
A
NH2
17
A
N
NH2
18
1_555
metalc
2.379
A
ASP
5
A
OD1
ASP
6
1_555
A
LA
18
B
LA
LA
1_555
metalc
2.383
A
GLU
12
A
OE2
GLU
13
1_555
A
LA
18
B
LA
LA
1_555
CALCIUM-BINDING
EF HAND CALCIUM BINDING LOOP, ALPHA-HELIX, CALCIUM-BINDING
CALM_HUMAN
UNP
1
1
P02593
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD
SEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
93
104
1NKF
1
12
P02593
A
1
2
13
1
ASN
conflict
ASP
5
1NKF
A
P02593
UNP
97
6
BINDING SITE FOR RESIDUE LA A 18
A
LA
18
Software
5
A
ASP
1
A
ASP
2
5
1_555
A
ASP
3
A
ASP
4
5
1_555
A
ASP
5
A
ASP
6
5
1_555
A
TYR
7
A
TYR
8
5
1_555
A
GLU
12
A
GLU
13
5
1_555
1
P 1