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SMTL ID : 5yg4.2
(1 other biounit)
Plasmodium vivax SHMT bound with PLP-glycine and S-GS849
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.30 Å
Oligo State
homo-dimer
Ligands
2 x
PLG
:
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
(Non-covalent)
PLG.1:
19 residues within 4Å:
Chain A:
S.34
,
S.100
,
G.101
,
S.102
,
H.129
,
Y.182
,
T.183
,
D.208
,
S.210
,
H.211
,
T.234
,
H.236
,
K.237
,
R.371
Chain B:
Y.54
,
E.56
,
Y.64
,
G.271
,
G.272
18
PLIP interactions
:
4 interactions with chain B
,
14 interactions with chain A
Hydrogen bonds:
B:Y.54
,
B:Y.64
,
B:G.271
,
B:G.272
,
A:S.34
,
A:G.101
,
A:S.102
,
A:N.105
,
A:T.183
,
A:S.210
Water bridges:
A:S.100
,
A:S.100
,
A:R.243
Salt bridges:
A:H.211
,
A:H.236
,
A:K.237
,
A:R.371
pi-Stacking:
A:H.129
PLG.5:
19 residues within 4Å:
Chain A:
Y.54
,
E.56
,
Y.64
,
G.271
,
G.272
Chain B:
S.34
,
S.100
,
G.101
,
S.102
,
H.129
,
Y.182
,
T.183
,
D.208
,
S.210
,
H.211
,
T.234
,
H.236
,
K.237
,
R.371
18
PLIP interactions
:
16 interactions with chain B
,
2 interactions with chain A
Hydrogen bonds:
B:S.34
,
B:G.101
,
B:S.102
,
B:N.105
,
B:T.183
,
B:T.183
,
B:S.210
,
A:G.271
,
A:G.272
Water bridges:
B:S.100
,
B:S.100
,
B:T.232
,
B:R.243
Salt bridges:
B:H.211
,
B:H.236
,
B:K.237
,
B:R.371
pi-Stacking:
B:H.129
2 x
8UF
:
2-[1-[(3~{S})-6'-azanyl-5'-cyano-7-fluoranyl-2,2,3'-trimethyl-spiro[1~{H}-indene-3,4'-2~{H}-pyrano[2,3-c]pyrazole]-5-yl]piperidin-4-yl]ethanoic acid
(Non-covalent)
8UF.2:
18 residues within 4Å:
Chain A:
L.124
,
G.127
,
G.128
,
H.129
,
L.130
,
V.141
,
T.183
,
S.184
,
N.354
,
K.355
,
N.356
,
T.357
,
C.364
,
R.371
Chain B:
E.56
,
Y.63
,
Y.64
,
P.267
10
PLIP interactions
:
7 interactions with chain A
,
3 interactions with chain B
Hydrophobic interactions:
A:L.124
,
A:L.130
,
A:V.141
,
B:Y.63
,
B:Y.64
Hydrogen bonds:
A:G.127
,
A:L.130
,
A:T.183
,
A:T.357
,
B:E.56
8UF.6:
18 residues within 4Å:
Chain A:
E.56
,
Y.63
,
Y.64
,
P.267
Chain B:
L.124
,
G.127
,
G.128
,
H.129
,
L.130
,
V.141
,
T.183
,
S.184
,
N.354
,
K.355
,
N.356
,
T.357
,
C.364
,
R.371
10
PLIP interactions
:
4 interactions with chain A
,
6 interactions with chain B
Hydrophobic interactions:
A:Y.63
,
A:Y.64
,
B:L.124
,
B:L.130
,
B:V.141
Hydrogen bonds:
A:E.56
,
B:G.127
,
B:L.130
,
B:T.357
Water bridges:
A:Y.63
2 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.3:
5 residues within 4Å:
Chain A:
N.276
,
K.277
Chain B:
N.276
,
K.277
Ligands:
CL.7
Ligand excluded by PLIP
CL.7:
5 residues within 4Å:
Chain A:
N.276
,
K.277
Chain B:
N.276
,
K.277
Ligands:
CL.3
Ligand excluded by PLIP
2 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.4:
6 residues within 4Å:
Chain A:
Q.78
,
G.93
,
V.94
,
F.249
,
E.258
,
N.262
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:V.94
,
A:N.262
,
A:N.262
Water bridges:
A:Q.78
GOL.8:
6 residues within 4Å:
Chain B:
Q.78
,
G.93
,
V.94
,
F.249
,
E.258
,
N.262
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:V.94
,
B:E.258
,
B:N.262
,
B:N.262
Water bridges:
B:Q.78
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Schwertz, G. et al., Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold. ChemMedChem (2018)
Release Date
2018-06-06
Peptides
Serine hydroxymethyltransferase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
C
B
C
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Secondary Structure
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Serine hydroxymethyltransferase
Toggle Identical (AB)
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