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SMTL ID : 1kji.1
Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-AMPPCP
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.60 Å
Oligo State
homo-dimer
Ligands
4 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
3 residues within 4Å:
Chain A:
E.278
Ligands:
MG.2
,
ACP.6
4
PLIP interactions
:
2 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:E.278
,
A:E.278
,
H
2
O.5
,
H
2
O.6
MG.2:
4 residues within 4Å:
Chain A:
E.266
,
E.278
Ligands:
MG.1
,
ACP.6
4
PLIP interactions
:
3 interactions with chain A
,
1 Ligand-Water interactions
Metal complexes:
A:E.266
,
A:E.266
,
A:E.278
,
H
2
O.3
MG.9:
3 residues within 4Å:
Chain B:
E.278
Ligands:
MG.10
,
ACP.12
4
PLIP interactions
:
2 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:E.278
,
B:E.278
,
H
2
O.23
,
H
2
O.26
MG.10:
4 residues within 4Å:
Chain B:
E.266
,
E.278
Ligands:
MG.9
,
ACP.12
4
PLIP interactions
:
3 interactions with chain B
,
1 Ligand-Water interactions
Metal complexes:
B:E.266
,
B:E.266
,
B:E.278
,
H
2
O.29
3 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.3:
2 residues within 4Å:
Chain A:
A.52
Chain B:
A.52
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:A.52
NA.4:
4 residues within 4Å:
Chain A:
E.94
,
L.98
,
N.99
,
V.100
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:E.94
,
A:N.99
,
A:V.100
NA.11:
4 residues within 4Å:
Chain B:
N.99
,
V.100
,
P.102
,
C.103
6
PLIP interactions
:
6 interactions with chain B
Hydrogen bonds:
B:N.99
,
B:V.100
,
B:P.102
Water bridges:
B:E.94
,
B:Y.260
,
B:Y.260
1 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.5:
3 residues within 4Å:
Chain A:
R.118
,
R.132
,
F.133
Ligand excluded by PLIP
2 x
ACP
:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
(Non-covalent)
ACP.6:
21 residues within 4Å:
Chain A:
R.113
,
S.129
,
I.152
,
K.154
,
S.158
,
S.159
,
S.160
,
G.161
,
Q.164
,
E.194
,
G.195
,
V.196
,
V.197
,
F.199
,
E.202
,
Q.224
,
E.266
,
F.268
,
E.278
Ligands:
MG.1
,
MG.2
20
PLIP interactions
:
20 interactions with chain A
Hydrogen bonds:
A:R.113
,
A:R.113
,
A:S.129
,
A:K.154
,
A:S.160
,
A:G.161
,
A:Q.164
,
A:E.194
,
A:V.197
,
A:E.202
Water bridges:
A:E.83
,
A:Q.224
,
A:E.266
,
A:E.266
,
A:E.266
,
A:E.278
,
A:E.278
,
A:H.284
Salt bridges:
A:R.113
,
A:K.154
ACP.12:
19 residues within 4Å:
Chain B:
R.113
,
S.129
,
K.154
,
S.158
,
S.159
,
S.160
,
G.161
,
Q.164
,
E.194
,
G.195
,
V.197
,
F.199
,
E.202
,
Q.224
,
E.266
,
F.268
,
E.278
Ligands:
MG.9
,
MG.10
18
PLIP interactions
:
18 interactions with chain B
Hydrogen bonds:
B:R.113
,
B:R.113
,
B:S.129
,
B:K.154
,
B:S.160
,
B:G.161
,
B:Q.164
,
B:E.194
,
B:V.197
,
B:E.202
,
B:E.278
Water bridges:
B:E.83
,
B:E.266
,
B:E.266
,
B:E.278
,
B:E.278
Salt bridges:
B:R.113
,
B:K.154
1 x
MPO
:
3[N-MORPHOLINO]PROPANE SULFONIC ACID
(Non-covalent)
MPO.7:
7 residues within 4Å:
Chain A:
D.45
,
M.49
,
H.50
,
R.54
,
S.55
Chain B:
L.7
,
H.53
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:S.55
Water bridges:
A:D.45
Salt bridges:
A:D.45
1 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.8:
3 residues within 4Å:
Chain A:
N.59
,
D.62
,
R.68
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:N.59
,
A:D.62
,
A:R.68
Water bridges:
A:R.42
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Thoden, J.B. et al., PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. J.Biol.Chem. (2002)
Release Date
2002-06-28
Peptides
phosphoribosylglycinamide formyltransferase 2:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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phosphoribosylglycinamide formyltransferase 2
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