1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Munoz, A.
Forsterling, F.H.
Shaw III, C.F.
Petering, D.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
Cd 2
112.411
CADMIUM ION
non-polymer
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 H15 N2 O2 1
147.195
y
LYSINE
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
GW
J.Biol.Inorg.Chem.
JJBCFA
2154
0949-8257
7
713
724
10.1007/s00775-002-0345-3
12203008
Structure of the (113)Cd(3)beta domains from Homarus americanus metallothionein-1: hydrogen bonding and solvent accessibility of sulfur atoms
2002
10.2210/pdb1j5m/pdb
pdb_00001j5m
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
2847.406
METALLOTHIONEIN-1
BETA_N DOMAIN (RESIDUES 1-28)
1
syn
polymer
112.411
CADMIUM ION
3
syn
non-polymer
CUMT-1
no
no
PGPCCKDKCECAEGGCKTGCKCTSCRCA
PGPCCKDKCECAEGGCKTGCKCTSCRCA
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
atom_site
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
database_2
pdbx_database_status
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Data collection
Database references
Derived calculations
Other
Database references
Derived calculations
Other
1
0
2002-05-22
1
1
2008-04-26
1
2
2011-07-13
2
0
2020-02-05
2
1
2023-06-14
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_atom_id
_atom_site.label_atom_id
_pdbx_database_status.status_code_cs
_pdbx_nmr_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
2002-05-22
SPRSDE
contains 1H, 13C chemical shifts and 3JHNHA and 3JHAHB coupling constants
contains the minimized average structure of the beta_C domain of this protein
RCSB
Y
RCSB
2002-05-16
REL
REL
REL
REL
CD
CADMIUM ION
The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homarus americanus (American lobster).
sample
HN-S hydrogen bonds were determined using a 2D long range 1H{113Cd} HMQC experiment
1
2D-TOCSY
2D-NOESY
DQF-COSY
PE-COSY
2D-113Cd-HSQC-TOCSY
2D-TOCSY
5mM Tris-HCl
7.4
ambient
278
K
5mM Tris-HCl
7.4
ambient
298
K
The structure is based on 276 distance restraints, 240 derived from NOE, 33 metal cluster
restraints from 113Cd HSQC TOCSY and 6 restraints from HN-S hydrogen bonds. A total of 27
dihedral angle restraints was applied, 13 phi, 10 chi1 and 4 Cys-Cd chi2 angles. Methylene
protons for which no stereospecific assignment could be obtained were treated with the
floating chirality procedure in XPLOR.
Ab initio simulated annealing
5mM (113Cd)3-beta_N, 5mM d-Tris-HCl
90% H2O/10% D2O
Bruker
collection
XwinNMR
2.5
Bruker
processing
XwinNMR
2.5
MSI
data analysis
Felix
2000
Axel Brunger
structure solution
X-PLOR
3.851
Reto Koradi
data analysis
MOLMOL
2k.1
Axel Brunger
refinement
X-PLOR
3.851
500
Bruker
DRX
300
Bruker
DPX
CD
29
2
CD
CD
29
A
CD
30
2
CD
CD
30
A
CD
31
2
CD
CD
31
A
PRO
1
n
1
PRO
1
A
GLY
2
n
2
GLY
2
A
PRO
3
n
3
PRO
3
A
CYS
4
n
4
CYS
4
A
CYS
5
n
5
CYS
5
A
LYS
6
n
6
LYS
6
A
ASP
7
n
7
ASP
7
A
LYS
8
n
8
LYS
8
A
CYS
9
n
9
CYS
9
A
GLU
10
n
10
GLU
10
A
CYS
11
n
11
CYS
11
A
ALA
12
n
12
ALA
12
A
GLU
13
n
13
GLU
13
A
GLY
14
n
14
GLY
14
A
GLY
15
n
15
GLY
15
A
CYS
16
n
16
CYS
16
A
LYS
17
n
17
LYS
17
A
THR
18
n
18
THR
18
A
GLY
19
n
19
GLY
19
A
CYS
20
n
20
CYS
20
A
LYS
21
n
21
LYS
21
A
CYS
22
n
22
CYS
22
A
THR
23
n
23
THR
23
A
SER
24
n
24
SER
24
A
CYS
25
n
25
CYS
25
A
ARG
26
n
26
ARG
26
A
CYS
27
n
27
CYS
27
A
ALA
28
n
28
ALA
28
A
author_defined_assembly
1
monomeric
A
CYS
4
A
SG
CYS
4
1_555
A
CD
30
C
CD
CD
1_555
A
CYS
5
A
SG
CYS
5
1_555
117.1
A
CYS
4
A
SG
CYS
4
1_555
A
CD
30
C
CD
CD
1_555
A
CYS
16
A
SG
CYS
16
1_555
110.3
A
CYS
5
A
SG
CYS
5
1_555
A
CD
30
C
CD
CD
1_555
A
CYS
16
A
SG
CYS
16
1_555
100.1
A
CYS
4
A
SG
CYS
4
1_555
A
CD
30
C
CD
CD
1_555
A
CYS
20
A
SG
CYS
20
1_555
109.4
A
CYS
5
A
SG
CYS
5
1_555
A
CD
30
C
CD
CD
1_555
A
CYS
20
A
SG
CYS
20
1_555
111.2
A
CYS
16
A
SG
CYS
16
1_555
A
CD
30
C
CD
CD
1_555
A
CYS
20
A
SG
CYS
20
1_555
108.2
A
CYS
5
A
SG
CYS
5
1_555
A
CD
29
B
CD
CD
1_555
A
CYS
9
A
SG
CYS
9
1_555
108.3
A
CYS
5
A
SG
CYS
5
1_555
A
CD
29
B
CD
CD
1_555
A
CYS
22
A
SG
CYS
22
1_555
106.7
A
CYS
9
A
SG
CYS
9
1_555
A
CD
29
B
CD
CD
1_555
A
CYS
22
A
SG
CYS
22
1_555
111.4
A
CYS
5
A
SG
CYS
5
1_555
A
CD
29
B
CD
CD
1_555
A
CYS
25
A
SG
CYS
25
1_555
116.0
A
CYS
9
A
SG
CYS
9
1_555
A
CD
29
B
CD
CD
1_555
A
CYS
25
A
SG
CYS
25
1_555
107.8
A
CYS
22
A
SG
CYS
22
1_555
A
CD
29
B
CD
CD
1_555
A
CYS
25
A
SG
CYS
25
1_555
106.7
A
CYS
11
A
SG
CYS
11
1_555
A
CD
31
D
CD
CD
1_555
A
CYS
16
A
SG
CYS
16
1_555
107.0
A
CYS
11
A
SG
CYS
11
1_555
A
CD
31
D
CD
CD
1_555
A
CYS
25
A
SG
CYS
25
1_555
107.1
A
CYS
16
A
SG
CYS
16
1_555
A
CD
31
D
CD
CD
1_555
A
CYS
25
A
SG
CYS
25
1_555
111.8
A
CYS
11
A
SG
CYS
11
1_555
A
CD
31
D
CD
CD
1_555
A
CYS
27
A
SG
CYS
27
1_555
110.7
A
CYS
16
A
SG
CYS
16
1_555
A
CD
31
D
CD
CD
1_555
A
CYS
27
A
SG
CYS
27
1_555
109.5
A
CYS
25
A
SG
CYS
25
1_555
A
CD
31
D
CD
CD
1_555
A
CYS
27
A
SG
CYS
27
1_555
110.6
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
ARG
26
0.316
SIDE CHAIN
1
A
CYS
4
-174.43
-171.75
1
A
CYS
5
40.27
29.10
1
A
ASP
7
-133.08
-35.18
1
A
LYS
8
-135.78
-103.78
1
A
CYS
9
175.33
149.20
1
A
GLU
10
-137.61
-77.84
1
A
CYS
11
50.37
19.05
1
A
GLU
13
-97.41
31.78
1
A
LYS
17
-128.26
-62.48
1
A
THR
18
-163.23
-75.33
1
A
CYS
20
-29.69
113.13
1
A
THR
23
-87.46
38.44
SOLUTION STRUCTURE OF THE SYNTHETIC 113CD_3 BETA_N DOMAIN OF LOBSTER METALLOTHIONEIN-1
1
N
N
2
N
N
2
N
N
2
N
N
metalc
2.569
A
CYS
4
A
SG
CYS
4
1_555
A
CD
30
C
CD
CD
1_555
metalc
2.557
A
CYS
5
A
SG
CYS
5
1_555
A
CD
29
B
CD
CD
1_555
metalc
2.542
A
CYS
5
A
SG
CYS
5
1_555
A
CD
30
C
CD
CD
1_555
metalc
2.557
A
CYS
9
A
SG
CYS
9
1_555
A
CD
29
B
CD
CD
1_555
metalc
2.540
A
CYS
11
A
SG
CYS
11
1_555
A
CD
31
D
CD
CD
1_555
metalc
2.529
A
CYS
16
A
SG
CYS
16
1_555
A
CD
30
C
CD
CD
1_555
metalc
2.534
A
CYS
16
A
SG
CYS
16
1_555
A
CD
31
D
CD
CD
1_555
metalc
2.551
A
CYS
20
A
SG
CYS
20
1_555
A
CD
30
C
CD
CD
1_555
metalc
2.556
A
CYS
22
A
SG
CYS
22
1_555
A
CD
29
B
CD
CD
1_555
metalc
2.581
A
CYS
25
A
SG
CYS
25
1_555
A
CD
29
B
CD
CD
1_555
metalc
2.582
A
CYS
25
A
SG
CYS
25
1_555
A
CD
31
D
CD
CD
1_555
metalc
2.562
A
CYS
27
A
SG
CYS
27
1_555
A
CD
31
D
CD
CD
1_555
METAL BINDING PROTEIN
Metallothionein, beta-domain, metal-sulfur-cluster, 2D-NMR, 113Cd-NMR, conformational changes, HN-S-hydrogen bonds, METAL BINDING PROTEIN
MT1_HOMAM
UNP
1
1
P29499
PGPCCKDKCECAEGGCKTGCKCTSCRCA
1
28
1J5M
1
28
P29499
A
1
1
28
BINDING SITE FOR RESIDUE CD A 29
A
CD
29
Software
4
BINDING SITE FOR RESIDUE CD A 30
A
CD
30
Software
4
BINDING SITE FOR RESIDUE CD A 31
A
CD
31
Software
4
A
CYS
5
A
CYS
5
4
1_555
A
CYS
9
A
CYS
9
4
1_555
A
CYS
22
A
CYS
22
4
1_555
A
CYS
25
A
CYS
25
4
1_555
A
CYS
4
A
CYS
4
4
1_555
A
CYS
5
A
CYS
5
4
1_555
A
CYS
16
A
CYS
16
4
1_555
A
CYS
20
A
CYS
20
4
1_555
A
CYS
11
A
CYS
11
4
1_555
A
CYS
16
A
CYS
16
4
1_555
A
CYS
25
A
CYS
25
4
1_555
A
CYS
27
A
CYS
27
4
1_555