Sodium in PDB 6pte: Crystal Structure of Ilnamitki Peptide Bound to Hla-A2
Protein crystallography data
The structure of Crystal Structure of Ilnamitki Peptide Bound to Hla-A2, PDB code: 6pte
was solved by
A.R.Smith,
A.Arbuiso,
G.L.J.Keller,
B.M.Baker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.82 /
1.90
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.429,
84.106,
85.363,
90.01,
90.06,
90.02
|
R / Rfree (%)
|
15.9 /
18.6
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2
(pdb code 6pte). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of Ilnamitki Peptide Bound to Hla-A2, PDB code: 6pte:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6pte
Go back to
Sodium Binding Sites List in 6pte
Sodium binding site 1 out
of 4 in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Ilnamitki Peptide Bound to Hla-A2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na201
b:36.5
occ:1.00
|
O
|
B:HOH391
|
2.4
|
32.0
|
1.0
|
O
|
B:LEU88
|
2.5
|
25.1
|
1.0
|
O
|
B:HOH386
|
2.5
|
31.6
|
1.0
|
O
|
B:HOH384
|
2.5
|
32.3
|
1.0
|
OD1
|
B:ASN84
|
2.6
|
22.5
|
1.0
|
O
|
B:HIS85
|
2.6
|
14.4
|
1.0
|
CG
|
B:ASN84
|
3.4
|
25.2
|
1.0
|
C
|
B:HIS85
|
3.5
|
15.0
|
1.0
|
C
|
B:LEU88
|
3.7
|
24.1
|
1.0
|
ND2
|
B:ASN84
|
3.7
|
26.1
|
1.0
|
N
|
B:HIS85
|
3.9
|
17.2
|
1.0
|
CA
|
B:VAL86
|
4.2
|
15.0
|
1.0
|
N
|
B:VAL86
|
4.3
|
14.4
|
1.0
|
N
|
B:LEU88
|
4.4
|
18.2
|
1.0
|
CA
|
B:HIS85
|
4.4
|
15.8
|
1.0
|
CA
|
B:LEU88
|
4.4
|
18.5
|
1.0
|
CB
|
B:LEU88
|
4.5
|
15.9
|
1.0
|
C
|
B:VAL86
|
4.5
|
15.0
|
1.0
|
O
|
B:VAL86
|
4.6
|
18.8
|
1.0
|
C
|
B:SER89
|
4.6
|
28.8
|
1.0
|
CB
|
B:ASN84
|
4.7
|
22.5
|
1.0
|
O
|
B:SER89
|
4.7
|
28.8
|
1.0
|
N
|
B:SER89
|
4.7
|
23.9
|
1.0
|
C
|
B:ASN84
|
4.8
|
18.2
|
1.0
|
CA
|
B:SER89
|
4.9
|
28.5
|
1.0
|
N
|
B:GLN90
|
4.9
|
25.8
|
1.0
|
CA
|
B:ASN84
|
5.0
|
14.9
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6pte
Go back to
Sodium Binding Sites List in 6pte
Sodium binding site 2 out
of 4 in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Ilnamitki Peptide Bound to Hla-A2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na201
b:30.4
occ:1.00
|
O
|
F:HOH388
|
2.4
|
21.9
|
1.0
|
O
|
F:LEU88
|
2.4
|
28.4
|
1.0
|
O
|
F:HIS85
|
2.4
|
16.3
|
1.0
|
O
|
F:HOH396
|
2.4
|
25.6
|
1.0
|
OD1
|
F:ASN84
|
2.5
|
19.0
|
1.0
|
O
|
F:HOH391
|
2.6
|
30.8
|
1.0
|
C
|
F:HIS85
|
3.4
|
14.8
|
1.0
|
CG
|
F:ASN84
|
3.4
|
22.5
|
1.0
|
C
|
F:LEU88
|
3.6
|
24.3
|
1.0
|
ND2
|
F:ASN84
|
3.7
|
26.4
|
1.0
|
N
|
F:HIS85
|
3.8
|
13.9
|
1.0
|
CA
|
F:VAL86
|
4.1
|
15.1
|
1.0
|
N
|
F:VAL86
|
4.1
|
13.4
|
1.0
|
N
|
F:LEU88
|
4.2
|
19.0
|
1.0
|
CA
|
F:LEU88
|
4.2
|
21.0
|
1.0
|
CA
|
F:HIS85
|
4.2
|
13.7
|
1.0
|
CB
|
F:LEU88
|
4.3
|
17.1
|
1.0
|
C
|
F:VAL86
|
4.3
|
16.5
|
1.0
|
O
|
F:VAL86
|
4.4
|
17.9
|
1.0
|
C
|
F:SER89
|
4.6
|
27.2
|
1.0
|
O
|
F:SER89
|
4.6
|
29.1
|
1.0
|
N
|
F:SER89
|
4.6
|
25.6
|
1.0
|
CB
|
F:ASN84
|
4.7
|
16.8
|
1.0
|
C
|
F:ASN84
|
4.8
|
12.2
|
1.0
|
CA
|
F:SER89
|
4.8
|
28.1
|
1.0
|
N
|
F:GLN90
|
4.9
|
24.0
|
1.0
|
CA
|
F:ASN84
|
4.9
|
12.8
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6pte
Go back to
Sodium Binding Sites List in 6pte
Sodium binding site 3 out
of 4 in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Ilnamitki Peptide Bound to Hla-A2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na201
b:30.3
occ:1.00
|
O
|
I:HOH385
|
2.4
|
34.0
|
1.0
|
O
|
I:HOH381
|
2.5
|
30.7
|
1.0
|
O
|
I:LEU88
|
2.5
|
22.9
|
1.0
|
O
|
I:HIS85
|
2.5
|
13.9
|
1.0
|
OD1
|
I:ASN84
|
2.6
|
22.5
|
1.0
|
CG
|
I:ASN84
|
3.4
|
24.7
|
1.0
|
C
|
I:HIS85
|
3.5
|
17.6
|
1.0
|
C
|
I:LEU88
|
3.7
|
24.5
|
1.0
|
ND2
|
I:ASN84
|
3.7
|
28.6
|
1.0
|
N
|
I:HIS85
|
3.8
|
16.7
|
1.0
|
CA
|
I:VAL86
|
4.2
|
14.2
|
1.0
|
N
|
I:VAL86
|
4.2
|
12.5
|
1.0
|
CA
|
I:HIS85
|
4.3
|
17.5
|
1.0
|
N
|
I:LEU88
|
4.4
|
18.2
|
1.0
|
CA
|
I:LEU88
|
4.4
|
19.6
|
1.0
|
CB
|
I:LEU88
|
4.5
|
17.4
|
1.0
|
C
|
I:VAL86
|
4.5
|
15.4
|
1.0
|
O
|
I:VAL86
|
4.5
|
18.9
|
1.0
|
CB
|
I:ASN84
|
4.7
|
19.9
|
1.0
|
C
|
I:SER89
|
4.7
|
30.4
|
1.0
|
O
|
I:SER89
|
4.7
|
31.6
|
1.0
|
C
|
I:ASN84
|
4.8
|
17.2
|
1.0
|
N
|
I:SER89
|
4.8
|
26.3
|
1.0
|
CA
|
I:ASN84
|
4.9
|
14.9
|
1.0
|
CA
|
I:SER89
|
5.0
|
30.7
|
1.0
|
N
|
I:GLN90
|
5.0
|
27.2
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6pte
Go back to
Sodium Binding Sites List in 6pte
Sodium binding site 4 out
of 4 in the Crystal Structure of Ilnamitki Peptide Bound to Hla-A2
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Ilnamitki Peptide Bound to Hla-A2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na201
b:26.7
occ:1.00
|
O
|
L:HOH392
|
2.4
|
28.7
|
1.0
|
O
|
L:HOH384
|
2.4
|
26.4
|
1.0
|
O
|
L:LEU88
|
2.4
|
23.6
|
1.0
|
OD1
|
L:ASN84
|
2.5
|
19.6
|
1.0
|
O
|
L:HIS85
|
2.5
|
17.6
|
1.0
|
O
|
L:HOH395
|
2.8
|
37.4
|
1.0
|
CG
|
L:ASN84
|
3.4
|
20.7
|
1.0
|
C
|
L:HIS85
|
3.5
|
15.3
|
1.0
|
C
|
L:LEU88
|
3.6
|
21.7
|
1.0
|
ND2
|
L:ASN84
|
3.6
|
23.5
|
1.0
|
N
|
L:HIS85
|
3.9
|
11.5
|
1.0
|
CA
|
L:VAL86
|
4.2
|
14.0
|
1.0
|
N
|
L:LEU88
|
4.2
|
16.9
|
1.0
|
N
|
L:VAL86
|
4.2
|
13.1
|
1.0
|
CA
|
L:LEU88
|
4.3
|
18.0
|
1.0
|
CB
|
L:LEU88
|
4.3
|
15.3
|
1.0
|
CA
|
L:HIS85
|
4.3
|
12.9
|
1.0
|
C
|
L:VAL86
|
4.4
|
15.8
|
1.0
|
O
|
L:VAL86
|
4.5
|
18.2
|
1.0
|
O
|
L:SER89
|
4.5
|
28.8
|
1.0
|
C
|
L:SER89
|
4.5
|
26.6
|
1.0
|
N
|
L:SER89
|
4.6
|
23.5
|
1.0
|
CB
|
L:ASN84
|
4.7
|
16.9
|
1.0
|
C
|
L:ASN84
|
4.8
|
11.8
|
1.0
|
CA
|
L:SER89
|
4.8
|
27.5
|
1.0
|
N
|
L:GLN90
|
4.9
|
24.5
|
1.0
|
CA
|
L:ASN84
|
4.9
|
11.1
|
1.0
|
|
Reference:
T.P.Riley,
G.L.J.Keller,
A.R.Smith,
L.M.Davancaze,
A.G.Arbuiso,
J.R.Devlin,
B.M.Baker.
Structure Based Prediction of Neoantigen Immunogenicity. Front Immunol V. 10 2047 2019.
ISSN: ESSN 1664-3224
PubMed: 31555277
DOI: 10.3389/FIMMU.2019.02047
Page generated: Tue Oct 8 12:45:02 2024
|