The phiX174 DNA binding protein J in two different capsid environments.
Coordinates
PDB Format
Method
X-RAY DIFFRACTION
3.50 Å
Oligo State
hetero-20-20-20-mer
Ligands
20 x
DC-
DA-
DA-
DA:
DNA (5'-D(P*CP*AP*AP*A)-3')(Non-covalent)
DC-DA-DA-DA.1:
13
residues within 4Å:
Chain A:
H.204,
E.208,
F.212
Chain C:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain D:
T.423,
R.425,
D.426
Ligands:
DC.2,
DC.5
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.8:
13
residues within 4Å:
Chain D:
H.204,
E.208,
F.212
Chain F:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain G:
T.423,
R.425,
D.426
Ligands:
DC.9,
DC.12
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.15:
13
residues within 4Å:
Chain G:
H.204,
E.208,
F.212
Chain I:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain J:
T.423,
R.425,
D.426
Ligands:
DC.16,
DC.19
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.22:
13
residues within 4Å:
Chain J:
H.204,
E.208,
F.212
Chain L:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain M:
T.423,
R.425,
D.426
Ligands:
DC.23,
DC.26
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.29:
13
residues within 4Å:
Chain A:
T.423,
R.425,
D.426
Chain M:
H.204,
E.208,
F.212
Chain O:
A.27,
R.28,
Y.31,
G.34,
Q.35
Ligands:
DC.30,
DC.33
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.36:
13
residues within 4Å:
Chain P:
H.204,
E.208,
F.212
Chain R:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain S:
T.423,
R.425,
D.426
Ligands:
DC.37,
DC.40
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.43:
13
residues within 4Å:
Chain S:
H.204,
E.208,
F.212
Chain U:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain V:
T.423,
R.425,
D.426
Ligands:
DC.44,
DC.47
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.50:
13
residues within 4Å:
Chain V:
H.204,
E.208,
F.212
Chain X:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain Y:
T.423,
R.425,
D.426
Ligands:
DC.51,
DC.54
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.57:
13
residues within 4Å:
Chain 0:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain 1:
T.423,
R.425,
D.426
Chain Y:
H.204,
E.208,
F.212
Ligands:
DC.58,
DC.61
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.64:
13
residues within 4Å:
Chain 1:
H.204,
E.208,
F.212
Chain 3:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain P:
T.423,
R.425,
D.426
Ligands:
DC.65,
DC.68
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.71:
13
residues within 4Å:
Chain 4:
H.204,
E.208,
F.212
Chain 6:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain 7:
T.423,
R.425,
D.426
Ligands:
DC.72,
DC.75
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.78:
13
residues within 4Å:
Chain 7:
H.204,
E.208,
F.212
Chain 9:
A.27,
R.28,
Y.31,
G.34,
Q.35
Ligands:
DC.79,
DC.82
Chain a:
T.423,
R.425,
D.426
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.85:
13
residues within 4Å:
Ligands:
DC.86,
DC.89
Chain a:
H.204,
E.208,
F.212
Chain c:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain d:
T.423,
R.425,
D.426
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.92:
13
residues within 4Å:
Ligands:
DC.93,
DC.96
Chain d:
H.204,
E.208,
F.212
Chain f:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain g:
T.423,
R.425,
D.426
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.99:
13
residues within 4Å:
Chain 4:
T.423,
R.425,
D.426
Ligands:
DC.100,
DC.103
Chain g:
H.204,
E.208,
F.212
Chain i:
A.27,
R.28,
Y.31,
G.34,
Q.35
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.106:
13
residues within 4Å:
Ligands:
DC.107,
DC.110
Chain j:
H.204,
E.208,
F.212
Chain l:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain m:
T.423,
R.425,
D.426
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.113:
13
residues within 4Å:
Ligands:
DC.114,
DC.117
Chain m:
H.204,
E.208,
F.212
Chain o:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain p:
T.423,
R.425,
D.426
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.120:
13
residues within 4Å:
Ligands:
DC.121,
DC.124
Chain p:
H.204,
E.208,
F.212
Chain r:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain s:
T.423,
R.425,
D.426
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.127:
13
residues within 4Å:
Ligands:
DC.128,
DC.131
Chain s:
H.204,
E.208,
F.212
Chain u:
A.27,
R.28,
Y.31,
G.34,
Q.35
Chain v:
T.423,
R.425,
D.426
Protein-ligand interaction information (PLIP) not available
DC-DA-DA-DA.134:
13
residues within 4Å:
Ligands:
DC.135,
DC.138
Chain j:
T.423,
R.425,
D.426
Chain v:
H.204,
E.208,
F.212
Chain x:
A.27,
R.28,
Y.31,
G.34,
Q.35
Protein-ligand interaction information (PLIP) not available
120 x
DC:
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-functional Binders)(Non-covalent)(Covalent)
DC.2:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.1
17 PLIP interactions:
5 interactions with chain D,
4 interactions with chain A,
2 interactions with chain C,
1 interactions with chain P,
2 interactions with chain F,
3 interactions with chain G
Salt bridges:
D:R.10,
D:R.412,
A:R.10,
C:K.21,
F:K.21,
G:R.10,
G:R.412
DC.3:
3
residues within 4Å:
Chain P:
R.10,
F.277
Ligands:
DC.39
Protein-ligand interaction information (PLIP) not available
DC.4:
3
residues within 4Å:
Chain A:
R.10,
F.277
Ligands:
DC.38
Protein-ligand interaction information (PLIP) not available
DC.5:
4
residues within 4Å:
Chain A:
K.167
Chain C:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.1
Protein-ligand interaction information (PLIP) not available
DC.6:
2
residues within 4Å:
Chain A:
D.242
Chain C:
K.25
Protein-ligand interaction information (PLIP) not available
DC.7:
5
residues within 4Å:
Chain C:
R.18,
K.21
Chain D:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.9:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.8
Protein-ligand interaction information (PLIP) not available
DC.10:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.11:
2
residues within 4Å:
Chain D:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.12:
4
residues within 4Å:
Chain D:
K.167
Chain F:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.8
Protein-ligand interaction information (PLIP) not available
DC.13:
2
residues within 4Å:
Chain D:
D.242
Chain F:
K.25
Protein-ligand interaction information (PLIP) not available
DC.14:
5
residues within 4Å:
Chain F:
R.18,
K.21
Chain G:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.16:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.15
Protein-ligand interaction information (PLIP) not available
DC.17:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.18:
2
residues within 4Å:
Chain G:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.19:
4
residues within 4Å:
Chain G:
K.167
Chain I:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.15
19 PLIP interactions:
5 interactions with chain M,
5 interactions with chain J,
1 interactions with chain A,
2 interactions with chain I,
2 interactions with chain G,
2 interactions with chain O,
2 interactions with chain L
Salt bridges:
M:R.10,
M:R.412,
J:R.10,
J:R.412,
A:R.412,
I:K.21,
O:K.21,
L:K.21
DC.20:
2
residues within 4Å:
Chain G:
D.242
Chain I:
K.25
Protein-ligand interaction information (PLIP) not available
DC.21:
5
residues within 4Å:
Chain I:
R.18,
K.21
Chain J:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.23:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.22
Protein-ligand interaction information (PLIP) not available
DC.24:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.25:
2
residues within 4Å:
Chain J:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.26:
4
residues within 4Å:
Chain J:
K.167
Chain L:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.22
Protein-ligand interaction information (PLIP) not available
DC.27:
2
residues within 4Å:
Chain J:
D.242
Chain L:
K.25
Protein-ligand interaction information (PLIP) not available
DC.28:
5
residues within 4Å:
Chain L:
R.18,
K.21
Chain M:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.30:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.29
Protein-ligand interaction information (PLIP) not available
DC.31:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.32:
2
residues within 4Å:
Chain M:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.33:
4
residues within 4Å:
Chain M:
K.167
Chain O:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.29
Protein-ligand interaction information (PLIP) not available
DC.34:
2
residues within 4Å:
Chain M:
D.242
Chain O:
K.25
Protein-ligand interaction information (PLIP) not available
DC.35:
5
residues within 4Å:
Chain A:
V.47,
R.412,
N.414
Chain O:
R.18,
K.21
Protein-ligand interaction information (PLIP) not available
DC.37:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.36
17 PLIP interactions:
2 interactions with chain R,
2 interactions with chain U,
3 interactions with chain V,
5 interactions with chain S,
4 interactions with chain P,
1 interactions with chain A
Protein-ligand interaction information (PLIP) not available
DC.39:
3
residues within 4Å:
Chain P:
R.10,
F.277
Ligands:
DC.3
Protein-ligand interaction information (PLIP) not available
DC.40:
4
residues within 4Å:
Chain P:
K.167
Chain R:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.36
Protein-ligand interaction information (PLIP) not available
DC.41:
2
residues within 4Å:
Chain P:
D.242
Chain R:
K.25
Protein-ligand interaction information (PLIP) not available
DC.42:
5
residues within 4Å:
Chain R:
R.18,
K.21
Chain S:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.44:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.43
Protein-ligand interaction information (PLIP) not available
DC.45:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.46:
2
residues within 4Å:
Chain S:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.47:
4
residues within 4Å:
Chain S:
K.167
Chain U:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.43
Protein-ligand interaction information (PLIP) not available
DC.48:
2
residues within 4Å:
Chain S:
D.242
Chain U:
K.25
Protein-ligand interaction information (PLIP) not available
DC.49:
5
residues within 4Å:
Chain U:
R.18,
K.21
Chain V:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.51:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.50
Protein-ligand interaction information (PLIP) not available
DC.52:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.53:
2
residues within 4Å:
Chain V:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.54:
4
residues within 4Å:
Chain V:
K.167
Chain X:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.50
19 PLIP interactions:
2 interactions with chain V,
5 interactions with chain 1,
1 interactions with chain P,
5 interactions with chain Y,
2 interactions with chain X,
2 interactions with chain 0,
2 interactions with chain 3
Salt bridges:
1:R.10,
1:R.412,
P:R.412,
Y:R.10,
Y:R.412,
X:K.21,
0:K.21,
3:K.21
DC.55:
2
residues within 4Å:
Chain V:
D.242
Chain X:
K.25
Protein-ligand interaction information (PLIP) not available
DC.56:
5
residues within 4Å:
Chain X:
R.18,
K.21
Chain Y:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.58:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.57
Protein-ligand interaction information (PLIP) not available
DC.59:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.60:
2
residues within 4Å:
Chain Y:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.61:
4
residues within 4Å:
Chain 0:
Q.35,
Q.36
Chain Y:
K.167
Ligands:
DC-DA-DA-DA.57
Protein-ligand interaction information (PLIP) not available
DC.62:
2
residues within 4Å:
Chain 0:
K.25
Chain Y:
D.242
Protein-ligand interaction information (PLIP) not available
DC.63:
5
residues within 4Å:
Chain 0:
R.18,
K.21
Chain 1:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.65:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.64
Protein-ligand interaction information (PLIP) not available
DC.66:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.67:
2
residues within 4Å:
Chain 1:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.68:
4
residues within 4Å:
Chain 1:
K.167
Chain 3:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.64
Protein-ligand interaction information (PLIP) not available
DC.69:
2
residues within 4Å:
Chain 1:
D.242
Chain 3:
K.25
Protein-ligand interaction information (PLIP) not available
DC.70:
5
residues within 4Å:
Chain 3:
R.18,
K.21
Chain P:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.72:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.71
17 PLIP interactions:
3 interactions with chain a,
5 interactions with chain 7,
2 interactions with chain 9,
2 interactions with chain 6,
4 interactions with chain 4,
1 interactions with chain j
Protein-ligand interaction information (PLIP) not available
DC.74:
3
residues within 4Å:
Chain 4:
R.10,
F.277
Ligands:
DC.108
Protein-ligand interaction information (PLIP) not available
DC.75:
4
residues within 4Å:
Chain 4:
K.167
Chain 6:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.71
Protein-ligand interaction information (PLIP) not available
DC.76:
2
residues within 4Å:
Chain 4:
D.242
Chain 6:
K.25
Protein-ligand interaction information (PLIP) not available
DC.77:
5
residues within 4Å:
Chain 6:
R.18,
K.21
Chain 7:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.79:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.78
Protein-ligand interaction information (PLIP) not available
DC.80:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.81:
2
residues within 4Å:
Chain 7:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.82:
4
residues within 4Å:
Chain 7:
K.167
Chain 9:
Q.35,
Q.36
Ligands:
DC-DA-DA-DA.78
Protein-ligand interaction information (PLIP) not available
DC.83:
2
residues within 4Å:
Chain 7:
D.242
Chain 9:
K.25
Protein-ligand interaction information (PLIP) not available
DC.84:
5
residues within 4Å:
Chain 9:
R.18,
K.21
Chain a:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.86:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.85
Protein-ligand interaction information (PLIP) not available
DC.87:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.88:
2
residues within 4Å:
Chain a:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.89:
4
residues within 4Å:
Ligands:
DC-DA-DA-DA.85
Chain a:
K.167
Chain c:
Q.35,
Q.36
19 PLIP interactions:
5 interactions with chain g,
2 interactions with chain f,
1 interactions with chain 4,
2 interactions with chain c,
5 interactions with chain d,
2 interactions with chain a,
2 interactions with chain i
Salt bridges:
g:R.10,
g:R.412,
f:K.21,
4:R.412,
c:K.21,
d:R.10,
d:R.412,
i:K.21
DC.90:
2
residues within 4Å:
Chain a:
D.242
Chain c:
K.25
Protein-ligand interaction information (PLIP) not available
DC.91:
5
residues within 4Å:
Chain c:
R.18,
K.21
Chain d:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.93:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.92
Protein-ligand interaction information (PLIP) not available
DC.94:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.95:
2
residues within 4Å:
Chain d:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.96:
4
residues within 4Å:
Ligands:
DC-DA-DA-DA.92
Chain d:
K.167
Chain f:
Q.35,
Q.36
Protein-ligand interaction information (PLIP) not available
DC.97:
2
residues within 4Å:
Chain d:
D.242
Chain f:
K.25
Protein-ligand interaction information (PLIP) not available
DC.98:
5
residues within 4Å:
Chain f:
R.18,
K.21
Chain g:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.100:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.99
Protein-ligand interaction information (PLIP) not available
DC.101:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.102:
2
residues within 4Å:
Chain g:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.103:
4
residues within 4Å:
Ligands:
DC-DA-DA-DA.99
Chain g:
K.167
Chain i:
Q.35,
Q.36
Protein-ligand interaction information (PLIP) not available
DC.104:
2
residues within 4Å:
Chain g:
D.242
Chain i:
K.25
Protein-ligand interaction information (PLIP) not available
DC.105:
5
residues within 4Å:
Chain 4:
V.47,
R.412,
N.414
Chain i:
R.18,
K.21
Protein-ligand interaction information (PLIP) not available
DC.107:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.106
17 PLIP interactions:
4 interactions with chain j,
3 interactions with chain p,
2 interactions with chain l,
5 interactions with chain m,
2 interactions with chain o,
1 interactions with chain 4
Salt bridges:
j:R.10,
p:R.10,
p:R.412,
l:K.21,
m:R.10,
m:R.412,
o:K.21
DC.108:
3
residues within 4Å:
Chain 4:
R.10,
F.277
Ligands:
DC.74
Protein-ligand interaction information (PLIP) not available
DC.109:
3
residues within 4Å:
Ligands:
DC.73
Chain j:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.110:
4
residues within 4Å:
Ligands:
DC-DA-DA-DA.106
Chain j:
K.167
Chain l:
Q.35,
Q.36
Protein-ligand interaction information (PLIP) not available
DC.111:
2
residues within 4Å:
Chain j:
D.242
Chain l:
K.25
Protein-ligand interaction information (PLIP) not available
DC.112:
5
residues within 4Å:
Chain l:
R.18,
K.21
Chain m:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.114:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.113
Protein-ligand interaction information (PLIP) not available
DC.115:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.116:
2
residues within 4Å:
Chain m:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.117:
4
residues within 4Å:
Ligands:
DC-DA-DA-DA.113
Chain m:
K.167
Chain o:
Q.35,
Q.36
Protein-ligand interaction information (PLIP) not available
DC.118:
2
residues within 4Å:
Chain m:
D.242
Chain o:
K.25
Protein-ligand interaction information (PLIP) not available
DC.119:
5
residues within 4Å:
Chain o:
R.18,
K.21
Chain p:
V.47,
R.412,
N.414
Protein-ligand interaction information (PLIP) not available
DC.121:
1
residues within 4Å:
Ligands:
DC-DA-DA-DA.120
Protein-ligand interaction information (PLIP) not available
DC.122:
0
residues within 4Å:
(No contacts)
Protein-ligand interaction information (PLIP) not available
DC.123:
2
residues within 4Å:
Chain p:
R.10,
F.277
Protein-ligand interaction information (PLIP) not available
DC.124:
4
residues within 4Å:
Ligands:
DC-DA-DA-DA.120
Chain p:
K.167
Chain r:
Q.35,
Q.36
19 PLIP interactions:
5 interactions with chain s,
1 interactions with chain j,
5 interactions with chain v,
2 interactions with chain r,
2 interactions with chain p,
2 interactions with chain u,
2 interactions with chain x