Calcium in PDB 6ztb: Crystal Structure of Human P-Cadherin EC1_EC2
Protein crystallography data
The structure of Crystal Structure of Human P-Cadherin EC1_EC2, PDB code: 6ztb
was solved by
J.M.Rondeau,
S.Lehmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
57.55 /
1.40
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.889,
76.522,
46.208,
90,
107.79,
90
|
R / Rfree (%)
|
19.8 /
21.4
|
Other elements in 6ztb:
The structure of Crystal Structure of Human P-Cadherin EC1_EC2 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin EC1_EC2
(pdb code 6ztb). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Crystal Structure of Human P-Cadherin EC1_EC2, PDB code: 6ztb:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 6ztb
Go back to
Calcium Binding Sites List in 6ztb
Calcium binding site 1 out
of 3 in the Crystal Structure of Human P-Cadherin EC1_EC2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Human P-Cadherin EC1_EC2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca401
b:17.9
occ:1.00
|
OD2
|
I:ASP302
|
2.3
|
20.6
|
1.0
|
OD2
|
I:ASP243
|
2.3
|
18.1
|
1.0
|
O
|
I:HIS211
|
2.3
|
21.5
|
1.0
|
OD1
|
I:ASN209
|
2.4
|
21.3
|
1.0
|
OD2
|
I:ASP241
|
2.4
|
19.0
|
1.0
|
O
|
I:ASN250
|
2.4
|
18.9
|
1.0
|
OD1
|
I:ASP241
|
2.5
|
18.6
|
1.0
|
CG
|
I:ASP241
|
2.8
|
17.9
|
1.0
|
CG
|
I:ASP302
|
3.3
|
21.9
|
1.0
|
CG
|
I:ASP243
|
3.4
|
16.9
|
1.0
|
C
|
I:HIS211
|
3.5
|
21.3
|
1.0
|
CG
|
I:ASN209
|
3.5
|
22.1
|
1.0
|
C
|
I:ASN250
|
3.6
|
20.0
|
1.0
|
CB
|
I:ASP302
|
3.7
|
18.9
|
1.0
|
CB
|
I:ASP243
|
3.7
|
17.3
|
1.0
|
ND2
|
I:ASN209
|
4.1
|
24.0
|
1.0
|
N
|
I:HIS211
|
4.2
|
18.6
|
1.0
|
O
|
I:HOH585
|
4.2
|
29.2
|
1.0
|
CA
|
I:HIS211
|
4.3
|
19.3
|
1.0
|
CB
|
I:ASP241
|
4.3
|
19.3
|
1.0
|
CB
|
I:HIS211
|
4.4
|
19.9
|
1.0
|
N
|
I:GLY251
|
4.4
|
17.9
|
1.0
|
OD1
|
I:ASP302
|
4.4
|
22.9
|
1.0
|
CA
|
I:ASN250
|
4.5
|
18.1
|
1.0
|
CA
|
I:GLY251
|
4.5
|
17.5
|
1.0
|
N
|
I:LYS212
|
4.5
|
20.2
|
1.0
|
OD1
|
I:ASP243
|
4.5
|
17.9
|
1.0
|
CA
|
I:LYS212
|
4.7
|
18.6
|
1.0
|
CB
|
I:ASN209
|
4.7
|
19.9
|
1.0
|
CA
|
I:ASN209
|
4.8
|
20.2
|
1.0
|
CB
|
I:ASN250
|
4.8
|
19.4
|
1.0
|
N
|
I:ASP243
|
4.8
|
18.4
|
1.0
|
C
|
I:LYS212
|
4.8
|
20.5
|
1.0
|
CA
|
I:ASP243
|
4.9
|
16.9
|
1.0
|
C
|
I:ASN209
|
4.9
|
23.9
|
1.0
|
|
Calcium binding site 2 out
of 3 in 6ztb
Go back to
Calcium Binding Sites List in 6ztb
Calcium binding site 2 out
of 3 in the Crystal Structure of Human P-Cadherin EC1_EC2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Human P-Cadherin EC1_EC2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca402
b:20.4
occ:0.87
|
OE1
|
I:GLU176
|
2.3
|
19.4
|
1.0
|
OD2
|
I:ASP210
|
2.3
|
21.3
|
1.0
|
OE1
|
I:GLU118
|
2.3
|
18.1
|
1.0
|
O
|
I:HOH528
|
2.4
|
21.6
|
1.0
|
O
|
I:HOH727
|
2.4
|
25.8
|
1.0
|
OD1
|
I:ASP174
|
2.4
|
21.3
|
1.0
|
CG
|
I:ASP210
|
3.1
|
20.4
|
1.0
|
OD1
|
I:ASP210
|
3.3
|
19.4
|
1.0
|
CG
|
I:ASP174
|
3.3
|
24.0
|
1.0
|
CD
|
I:GLU118
|
3.3
|
18.3
|
1.0
|
CD
|
I:GLU176
|
3.5
|
19.7
|
1.0
|
OE2
|
I:GLU118
|
3.7
|
18.8
|
1.0
|
OD2
|
I:ASP174
|
3.9
|
26.4
|
1.0
|
CE1
|
I:HIS211
|
4.0
|
23.2
|
1.0
|
CA
|
I:CA403
|
4.0
|
17.4
|
1.0
|
O
|
I:HOH569
|
4.1
|
35.2
|
1.0
|
N
|
I:ARG175
|
4.1
|
17.9
|
1.0
|
CA
|
I:ASP174
|
4.1
|
18.8
|
1.0
|
CB
|
I:ASP174
|
4.1
|
20.5
|
1.0
|
N
|
I:GLU176
|
4.2
|
18.9
|
1.0
|
OD1
|
I:ASN119
|
4.3
|
20.5
|
1.0
|
ND2
|
I:ASN119
|
4.3
|
20.3
|
1.0
|
OE2
|
I:GLU176
|
4.4
|
19.6
|
1.0
|
CB
|
I:GLU176
|
4.4
|
20.3
|
1.0
|
C
|
I:ASP174
|
4.4
|
19.7
|
1.0
|
CG
|
I:GLU176
|
4.5
|
20.4
|
1.0
|
O
|
I:HOH755
|
4.5
|
52.4
|
1.0
|
CG
|
I:GLU118
|
4.6
|
18.6
|
1.0
|
O
|
I:HOH581
|
4.6
|
39.2
|
1.0
|
CB
|
I:ASP210
|
4.6
|
20.4
|
1.0
|
ND1
|
I:HIS211
|
4.6
|
23.4
|
1.0
|
CG
|
I:ASN119
|
4.8
|
18.5
|
1.0
|
O
|
I:HOH504
|
4.8
|
44.2
|
1.0
|
CA
|
I:GLU176
|
4.9
|
19.6
|
1.0
|
CB
|
I:GLU118
|
5.0
|
17.0
|
1.0
|
|
Calcium binding site 3 out
of 3 in 6ztb
Go back to
Calcium Binding Sites List in 6ztb
Calcium binding site 3 out
of 3 in the Crystal Structure of Human P-Cadherin EC1_EC2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Human P-Cadherin EC1_EC2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca403
b:17.4
occ:1.00
|
OD1
|
I:ASP243
|
2.3
|
17.9
|
1.0
|
OE2
|
I:GLU118
|
2.3
|
18.8
|
1.0
|
OD1
|
I:ASP207
|
2.3
|
18.3
|
1.0
|
OD1
|
I:ASP210
|
2.3
|
19.4
|
1.0
|
OE2
|
I:GLU176
|
2.4
|
19.6
|
1.0
|
O
|
I:GLN208
|
2.5
|
18.5
|
1.0
|
OE1
|
I:GLU176
|
2.8
|
19.4
|
1.0
|
CD
|
I:GLU176
|
2.9
|
19.7
|
1.0
|
CG
|
I:ASP207
|
3.4
|
16.7
|
1.0
|
CD
|
I:GLU118
|
3.4
|
18.3
|
1.0
|
CG
|
I:ASP243
|
3.4
|
16.9
|
1.0
|
CG
|
I:ASP210
|
3.5
|
20.4
|
1.0
|
C
|
I:GLN208
|
3.7
|
19.7
|
1.0
|
OE1
|
I:GLU118
|
3.8
|
18.1
|
1.0
|
OD2
|
I:ASP207
|
3.9
|
18.1
|
1.0
|
N
|
I:GLN208
|
3.9
|
17.7
|
1.0
|
CA
|
I:CA402
|
4.0
|
20.4
|
0.9
|
OD2
|
I:ASP210
|
4.1
|
21.3
|
1.0
|
CB
|
I:ASP243
|
4.1
|
17.3
|
1.0
|
N
|
I:ASP210
|
4.1
|
19.2
|
1.0
|
ND1
|
I:HIS211
|
4.1
|
23.4
|
1.0
|
CA
|
I:ASP243
|
4.3
|
16.9
|
1.0
|
CG
|
I:GLU176
|
4.4
|
20.4
|
1.0
|
CA
|
I:GLN208
|
4.4
|
18.3
|
1.0
|
OD2
|
I:ASP243
|
4.4
|
18.1
|
1.0
|
NE
|
I:ARG175
|
4.5
|
20.9
|
1.0
|
CB
|
I:ASP207
|
4.6
|
17.7
|
1.0
|
CB
|
I:ASP210
|
4.6
|
20.4
|
1.0
|
CE1
|
I:HIS211
|
4.6
|
23.2
|
1.0
|
CA
|
I:ASP207
|
4.7
|
16.2
|
1.0
|
NH2
|
I:ARG175
|
4.7
|
20.4
|
1.0
|
CG
|
I:GLU118
|
4.7
|
18.6
|
1.0
|
N
|
I:ASN209
|
4.7
|
20.2
|
1.0
|
CA
|
I:ASP210
|
4.8
|
19.1
|
1.0
|
C
|
I:ASP207
|
4.8
|
18.3
|
1.0
|
CA
|
I:ASN209
|
4.9
|
20.2
|
1.0
|
CB
|
I:ARG175
|
5.0
|
18.3
|
1.0
|
C
|
I:ASN209
|
5.0
|
23.9
|
1.0
|
N
|
I:ASP243
|
5.0
|
18.4
|
1.0
|
|
Reference:
Q.Sheng,
J.A.D'alessio,
D.L.Menezes,
C.Karim,
Y.Tang,
A.Tam,
S.Clark,
C.Ying,
A.Connor,
K.G.Mansfield,
J.M.Rondeau,
M.Ghoddusi,
F.C.Geyer,
J.Gu,
M.E.Mclaughlin,
R.Newcombe,
G.Elliott,
W.R.Tschantz,
S.Lehmann,
K.Miller,
T.Huber,
K.G.Rendahl,
U.Jeffry,
N.K.Pryer,
E.Lees,
P.Kwon,
J.A.Abraham,
J.S.Damiano,
T.J.Abrams.
PCA062, A P-Cadherin Targeting Antibody-Drug-Conjugate, Displays Potent Anti-Tumor Activity Against P-Cadherin-Expressing Malignancies. Mol.Cancer Ther. 2021.
ISSN: ESSN 1538-8514
PubMed: 33879555
DOI: 10.1158/1535-7163.MCT-20-0708
Page generated: Thu Jul 18 22:46:38 2024
|