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SMTL ID : 3gfx.1
Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.40 Å
Oligo State
homo-dimer
Ligands
2 x
FMN
:
FLAVIN MONONUCLEOTIDE
(Non-covalent)
FMN.1:
16 residues within 4Å:
Chain A:
Y.15
,
L.31
,
R.34
,
A.35
,
K.38
,
N.39
,
F.55
,
Q.57
,
L.59
,
L.69
,
E.72
,
I.73
,
D.76
,
R.78
,
H.79
,
M.100
14
PLIP interactions
:
14 interactions with chain A
Hydrophobic interactions:
A:L.31
,
A:F.55
,
A:R.78
Hydrogen bonds:
A:K.38
,
A:N.39
,
A:N.39
,
A:Q.57
,
A:D.76
,
A:D.76
,
A:R.78
Water bridges:
A:R.34
,
A:R.34
,
A:R.78
Salt bridges:
A:K.38
FMN.4:
16 residues within 4Å:
Chain B:
Y.15
,
L.31
,
R.34
,
A.35
,
K.38
,
N.39
,
F.55
,
Q.57
,
L.59
,
L.69
,
E.72
,
I.73
,
D.76
,
R.78
,
H.79
,
M.100
13
PLIP interactions
:
13 interactions with chain B
Hydrophobic interactions:
B:L.31
,
B:F.55
,
B:R.78
Hydrogen bonds:
B:K.38
,
B:N.39
,
B:N.39
,
B:Q.57
,
B:D.76
,
B:D.76
,
B:R.78
Water bridges:
B:R.78
Salt bridges:
B:R.34
,
B:K.38
2 x
C2E
:
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
(Non-covalent)
C2E.2:
22 residues within 4Å:
Chain A:
F.179
,
Q.182
,
E.196
,
A.197
,
L.198
,
I.199
,
R.200
,
P.207
,
F.211
,
D.223
,
K.227
,
N.247
,
L.249
,
D.310
,
D.311
,
G.368
,
V.369
,
E.370
,
G.388
,
F.389
,
P.394
Ligands:
CA.3
18
PLIP interactions
:
18 interactions with chain A
Hydrogen bonds:
A:Q.182
,
A:I.199
,
A:K.227
,
A:K.227
,
A:N.247
,
A:N.247
,
A:F.389
Water bridges:
A:E.367
,
A:E.367
,
A:E.370
,
A:E.370
,
A:Q.387
,
A:Q.387
Salt bridges:
A:R.200
,
A:D.223
,
A:E.370
pi-Stacking:
A:F.389
,
A:F.389
C2E.5:
20 residues within 4Å:
Chain B:
Q.182
,
E.196
,
L.198
,
I.199
,
R.200
,
P.207
,
F.211
,
D.223
,
K.227
,
N.247
,
L.249
,
D.310
,
D.311
,
G.368
,
V.369
,
E.370
,
G.388
,
F.389
,
P.394
Ligands:
CA.6
15
PLIP interactions
:
15 interactions with chain B
Hydrogen bonds:
B:Q.182
,
B:I.199
,
B:K.227
,
B:K.227
,
B:N.247
,
B:L.249
,
B:F.389
Water bridges:
B:D.310
,
B:D.310
,
B:D.311
,
B:D.311
Salt bridges:
B:R.200
,
B:D.223
,
B:E.370
pi-Stacking:
B:F.389
2 x
CA
:
CALCIUM ION
(Non-covalent)
CA.3:
5 residues within 4Å:
Chain A:
E.196
,
N.247
,
E.280
,
D.310
Ligands:
C2E.2
5
PLIP interactions
:
3 interactions with chain A
,
1 Ligand-Water interactions
,
1 Ligand-Ligand interactions
Metal complexes:
A:E.196
,
A:E.280
,
A:D.310
,
H
2
O.1
,
C2E.2
CA.6:
5 residues within 4Å:
Chain B:
E.196
,
N.247
,
E.280
,
D.310
Ligands:
C2E.5
5
PLIP interactions
:
3 interactions with chain B
,
1 Ligand-Ligand interactions
,
1 Ligand-Water interactions
Metal complexes:
B:E.196
,
B:E.280
,
B:D.310
,
C2E.5
,
H
2
O.9
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Barends, T.R. et al., Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature (2009)
Release Date
2009-06-23
Peptides
Klebsiella pneumoniae BlrP1:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Klebsiella pneumoniae BlrP1
Related Entries With Identical Sequence
3gfy.1
|
3gfz.1
|
3gg0.1
|
3gg1.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
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Outline
Fog
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