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SMTL ID : 4h2t.1
Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with cognate carrier protein and an analogue of glycyl adenylate
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.44 Å
Oligo State
hetero-oligomer
Ligands
2 x
ZN
:
ZINC ION
(Non-covalent)
ZN.1:
4 residues within 4Å:
Chain A:
C.151
,
E.196
,
C.299
Ligands:
G5A.2
3
PLIP interactions
:
3 interactions with chain A
Metal complexes:
A:C.151
,
A:E.196
,
A:C.299
ZN.3:
4 residues within 4Å:
Chain B:
C.151
,
E.196
,
C.299
Ligands:
G5A.4
3
PLIP interactions
:
3 interactions with chain B
Metal complexes:
B:C.151
,
B:E.196
,
B:C.299
2 x
G5A
:
5'-O-(GLYCYLSULFAMOYL)ADENOSINE
(Non-covalent)
G5A.2:
23 residues within 4Å:
Chain A:
A.149
,
C.151
,
R.179
,
E.181
,
D.187
,
R.188
,
L.189
,
F.192
,
M.194
,
E.196
,
D.235
,
K.255
,
A.270
,
C.271
,
M.272
,
S.273
,
N.275
,
C.299
,
A.301
,
G.303
,
R.306
Ligands:
ZN.1
,
PNS.7
24
PLIP interactions
:
24 interactions with chain A
Hydrogen bonds:
A:R.179
,
A:E.181
,
A:E.181
,
A:R.188
,
A:L.189
,
A:E.196
,
A:D.235
,
A:K.255
,
A:A.270
,
A:S.273
,
A:S.273
,
A:N.275
,
A:G.303
,
A:R.306
Water bridges:
A:R.179
,
A:R.179
,
A:R.179
,
A:R.306
Salt bridges:
A:R.179
,
A:K.255
pi-Stacking:
A:F.192
,
A:F.192
pi-Cation interactions:
A:R.306
,
A:R.306
G5A.4:
22 residues within 4Å:
Chain B:
A.149
,
C.151
,
R.179
,
E.181
,
D.187
,
R.188
,
L.189
,
F.192
,
M.194
,
E.196
,
K.255
,
A.270
,
C.271
,
M.272
,
S.273
,
N.275
,
C.299
,
A.301
,
G.303
,
R.306
Ligands:
ZN.3
,
PNS.8
16
PLIP interactions
:
16 interactions with chain B
Hydrogen bonds:
B:R.179
,
B:R.179
,
B:E.181
,
B:L.189
,
B:E.196
,
B:K.255
,
B:A.270
,
B:S.273
,
B:S.273
,
B:N.275
Salt bridges:
B:R.179
,
B:K.255
pi-Stacking:
B:F.192
,
B:F.192
pi-Cation interactions:
B:R.306
,
B:R.306
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.5:
2 residues within 4Å:
Chain B:
E.121
,
S.138
2
PLIP interactions
:
2 interactions with chain B
Water bridges:
B:R.128
,
B:R.128
SO4.6:
3 residues within 4Å:
Chain B:
A.71
,
R.86
,
R.195
4
PLIP interactions
:
4 interactions with chain B
Water bridges:
B:T.75
,
B:R.195
Salt bridges:
B:R.86
,
B:R.195
2 x
PNS
:
4'-PHOSPHOPANTETHEINE
(Covalent)
PNS.7:
11 residues within 4Å:
Chain A:
Y.152
,
D.235
,
F.237
,
Q.249
,
H.277
,
H.280
,
F.281
Chain C:
T.61
,
S.62
,
M.63
Ligands:
G5A.2
6
PLIP interactions
:
4 interactions with chain A
,
2 interactions with chain C
Hydrogen bonds:
A:Y.152
,
A:Q.249
,
A:Q.252
,
A:H.277
,
C:S.62
,
C:M.63
PNS.8:
13 residues within 4Å:
Chain B:
Y.152
,
D.235
,
F.237
,
Q.249
,
Q.252
,
L.254
,
H.277
,
R.278
,
H.280
Chain D:
T.61
,
S.62
,
M.63
Ligands:
G5A.4
7
PLIP interactions
:
5 interactions with chain B
,
2 interactions with chain D
Hydrophobic interactions:
B:H.280
Hydrogen bonds:
B:D.235
,
B:Q.249
,
B:H.277
,
D:S.62
,
D:M.63
Salt bridges:
B:R.278
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Mocibob, M. et al., Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation. Structure (2013)
Release Date
2013-03-06
Peptides
Amino acid--[acyl-carrier-protein] ligase 1:
A
B
Aminoacyl carrier protein 1:
C
D
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
C
C
D
D
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Secondary Structure
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2° Structure
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Amino acid--[acyl-carrier-protein] ligase 1
Aminoacyl carrier protein 1
Related Entries With Identical Sequence
3mey.1
|
3mf1.1
|
3mf2.1
|
3pzc.1
|
4h2s.1
|
4h2u.1
|
4h2v.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
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Transparent
Resolution
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