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SMTL ID : 7ocp.1
NADPH bound to the dehydrogenase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD from Acinetobacter baumannii
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.75 Å
Oligo State
homo-dimer
Ligands
1 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.1:
4 residues within 4Å:
Chain A:
K.405
,
E.406
,
H.407
,
Y.408
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:H.407
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
5 residues within 4Å:
Chain A:
D.16
,
D.18
,
E.175
,
D.176
Ligands:
SO4.3
3
PLIP interactions
:
3 interactions with chain A
Metal complexes:
A:D.16
,
A:D.18
,
A:D.176
MG.10:
7 residues within 4Å:
Chain B:
D.16
,
D.18
,
E.25
,
G.54
,
E.175
,
D.176
,
S.177
3
PLIP interactions
:
3 interactions with chain B
Metal complexes:
B:D.16
,
B:D.18
,
B:D.176
3 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.3:
6 residues within 4Å:
Chain A:
D.16
,
S.119
,
K.151
,
E.175
,
S.177
Ligands:
MG.2
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:S.119
,
A:E.175
,
A:S.177
Salt bridges:
A:K.151
SO4.5:
5 residues within 4Å:
Chain A:
N.374
,
K.375
,
R.613
,
K.614
,
R.620
4
PLIP interactions
:
4 interactions with chain A
Salt bridges:
A:K.375
,
A:R.613
,
A:K.614
,
A:R.620
SO4.9:
5 residues within 4Å:
Chain B:
R.609
,
R.613
,
K.614
,
R.620
Ligands:
NDP.8
4
PLIP interactions
:
4 interactions with chain B
Salt bridges:
B:R.609
,
B:R.613
,
B:K.614
,
B:R.620
2 x
NDP
:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
(Non-covalent)
NDP.4:
23 residues within 4Å:
Chain A:
G.251
,
F.252
,
G.253
,
A.254
,
I.255
,
S.279
,
T.280
,
R.281
,
N.282
,
C.335
,
L.336
,
P.337
,
A.340
,
S.343
,
E.344
,
I.372
,
L.373
,
N.374
,
V.414
,
R.416
,
M.417
,
V.418
,
K.420
17
PLIP interactions
:
17 interactions with chain A
Hydrophobic interactions:
A:I.255
Hydrogen bonds:
A:G.251
,
A:A.254
,
A:I.255
,
A:T.280
,
A:R.281
,
A:R.281
,
A:N.282
,
A:L.336
,
A:S.343
,
A:N.374
,
A:V.418
,
A:V.418
Salt bridges:
A:R.281
,
A:K.420
pi-Cation interactions:
A:R.281
,
A:R.281
NDP.8:
24 residues within 4Å:
Chain B:
G.251
,
F.252
,
G.253
,
A.254
,
I.255
,
T.280
,
R.281
,
N.282
,
C.335
,
L.336
,
P.337
,
A.340
,
E.344
,
I.372
,
L.373
,
N.374
,
V.414
,
R.416
,
M.417
,
V.418
,
K.420
,
R.606
,
R.609
Ligands:
SO4.9
21
PLIP interactions
:
21 interactions with chain B
Hydrophobic interactions:
B:I.255
,
B:V.414
Hydrogen bonds:
B:G.251
,
B:A.254
,
B:I.255
,
B:T.280
,
B:T.280
,
B:R.281
,
B:R.281
,
B:N.282
,
B:L.336
,
B:N.374
,
B:V.418
,
B:V.418
,
B:R.606
,
B:R.606
Salt bridges:
B:R.281
,
B:K.420
,
B:R.609
,
B:R.609
pi-Cation interactions:
B:R.281
2 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.6:
4 residues within 4Å:
Chain A:
G.99
,
Q.102
,
N.243
,
Q.244
Ligand excluded by PLIP
CL.11:
4 residues within 4Å:
Chain B:
G.99
,
Q.102
,
N.243
,
Q.244
Ligand excluded by PLIP
1 x
EPE
:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
(Non-functional Binders)
EPE.7:
10 residues within 4Å:
Chain A:
I.130
,
N.133
,
Y.135
Chain B:
R.298
,
L.421
,
N.425
,
Q.429
,
K.433
,
I.489
,
H.492
3
PLIP interactions
:
1 interactions with chain A
,
2 interactions with chain B
Hydrogen bonds:
A:N.133
Salt bridges:
B:R.298
,
B:K.433
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Tam, H.K. et al., Unidirectional mannitol synthesis of Acinetobacter baumannii MtlD is facilitated by the helix-loop-helix-mediated dimer formation. Proc.Natl.Acad.Sci.USA (2022)
Release Date
2022-04-20
Peptides
HAD hydrolase, family IA, variant 3:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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HAD hydrolase, family IA, variant 3
Related Entries With Identical Sequence
7ocn.1
|
7ocq.1
|
7ocr.1
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Tube
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