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SMTL ID : 6nne.3
(2 other biounits)
Crystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in complex with diaverdine
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.60 Å
Oligo State
homo-dimer
Ligands
2 x
CO
:
COBALT (II) ION
(Non-covalent)
CO.1:
4 residues within 4Å:
Chain A:
I.34
,
H.38
,
E.90
Chain B:
H.157
6
PLIP interactions
:
1 interactions with chain B
,
1 interactions with chain A
,
4 Ligand-Water interactions
Metal complexes:
B:H.157
,
A:H.38
,
H
2
O.1
,
H
2
O.3
,
H
2
O.3
,
H
2
O.8
CO.6:
3 residues within 4Å:
Chain B:
I.34
,
H.38
,
E.90
6
PLIP interactions
:
1 interactions with chain B
,
5 Ligand-Water interactions
Metal complexes:
B:H.38
,
H
2
O.4
,
H
2
O.6
,
H
2
O.6
,
H
2
O.8
,
H
2
O.8
2 x
NDP
:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
(Non-covalent)
NDP.2:
28 residues within 4Å:
Chain A:
W.6
,
A.7
,
I.14
,
G.15
,
R.16
,
G.18
,
D.19
,
I.20
,
W.22
,
G.43
,
R.44
,
R.45
,
T.46
,
L.65
,
S.66
,
R.67
,
Q.68
,
G.80
,
I.94
,
G.95
,
G.96
,
G.97
,
Q.98
,
V.99
,
Y.100
,
L.102
,
A.126
Ligands:
KUP.3
32
PLIP interactions
:
32 interactions with chain A
Hydrophobic interactions:
A:I.20
,
A:T.46
Hydrogen bonds:
A:A.7
,
A:I.14
,
A:R.16
,
A:G.18
,
A:G.18
,
A:G.43
,
A:R.44
,
A:R.44
,
A:R.45
,
A:T.46
,
A:T.46
,
A:R.67
,
A:R.67
,
A:R.67
,
A:Q.68
,
A:Q.68
,
A:G.96
,
A:G.97
,
A:Q.98
,
A:V.99
Water bridges:
A:G.15
,
A:R.45
,
A:R.45
,
A:S.49
,
A:R.67
,
A:R.67
Salt bridges:
A:R.44
,
A:R.45
pi-Cation interactions:
A:R.67
,
A:R.67
NDP.7:
27 residues within 4Å:
Chain B:
W.6
,
A.7
,
I.14
,
G.15
,
R.16
,
G.18
,
D.19
,
I.20
,
G.43
,
R.44
,
R.45
,
T.46
,
L.65
,
S.66
,
R.67
,
Q.68
,
G.80
,
I.94
,
G.95
,
G.96
,
G.97
,
Q.98
,
V.99
,
Y.100
,
L.102
,
A.126
Ligands:
KUP.8
31
PLIP interactions
:
31 interactions with chain B
Hydrophobic interactions:
B:I.20
,
B:T.46
Hydrogen bonds:
B:A.7
,
B:I.14
,
B:R.16
,
B:G.18
,
B:G.18
,
B:G.43
,
B:R.44
,
B:R.44
,
B:R.45
,
B:R.45
,
B:T.46
,
B:T.46
,
B:S.66
,
B:R.67
,
B:R.67
,
B:R.67
,
B:Q.68
,
B:Q.68
,
B:G.96
,
B:G.97
,
B:Q.98
,
B:V.99
Water bridges:
B:R.16
,
B:S.49
,
B:L.82
Salt bridges:
B:R.44
,
B:R.45
pi-Cation interactions:
B:R.67
,
B:R.67
2 x
KUP
:
5-[(3,4-dimethoxyphenyl)methyl]pyrimidine-2,4-diamine
(Non-covalent)
KUP.3:
14 residues within 4Å:
Chain A:
I.5
,
W.6
,
A.7
,
I.20
,
R.23
,
D.27
,
Q.28
,
F.31
,
L.50
,
L.57
,
I.94
,
Y.100
,
T.113
Ligands:
NDP.2
10
PLIP interactions
:
10 interactions with chain A
Hydrophobic interactions:
A:I.20
,
A:F.31
Hydrogen bonds:
A:I.5
,
A:W.6
,
A:Q.28
,
A:Y.100
,
A:T.113
Water bridges:
A:T.113
Salt bridges:
A:D.27
pi-Stacking:
A:F.31
KUP.8:
13 residues within 4Å:
Chain B:
I.5
,
W.6
,
A.7
,
I.20
,
D.27
,
Q.28
,
F.31
,
S.49
,
L.50
,
L.57
,
I.94
,
Y.100
Ligands:
NDP.7
12
PLIP interactions
:
12 interactions with chain B
Hydrophobic interactions:
B:I.20
,
B:F.31
,
B:F.31
,
B:L.50
Hydrogen bonds:
B:I.5
,
B:W.6
,
B:A.7
,
B:Q.28
,
B:Y.100
Water bridges:
B:T.113
Salt bridges:
B:D.27
pi-Stacking:
B:F.31
4 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.4:
2 residues within 4Å:
Chain A:
R.44
,
R.45
2
PLIP interactions
:
2 interactions with chain A
Salt bridges:
A:R.44
,
A:R.45
SO4.5:
2 residues within 4Å:
Chain A:
R.23
,
P.51
1
PLIP interactions
:
1 interactions with chain A
Salt bridges:
A:R.23
SO4.9:
3 residues within 4Å:
Chain A:
R.136
Chain B:
E.26
,
A.29
3
PLIP interactions
:
1 interactions with chain A
,
2 interactions with chain B
Hydrogen bonds:
A:R.136
,
B:R.146
Water bridges:
B:H.30
SO4.10:
2 residues within 4Å:
Chain B:
R.44
,
R.45
3
PLIP interactions
:
3 interactions with chain B
Water bridges:
B:R.44
Salt bridges:
B:R.44
,
B:R.45
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Ribeiro, J.A. et al., Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates. Acta Crystallogr D Struct Biol (2019)
Release Date
2019-07-17
Peptides
Dihydrofolate reductase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Dihydrofolate reductase
Toggle Identical (AB)
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|
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|
8cqa.1
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