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SMTL ID : 4pfn.2
(1 other biounit)
Crystal structure of Plasmodium vivax SHMT with L-serine Schiff base
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.50 Å
Oligo State
homo-dimer
Ligands
2 x
PLP
:
PYRIDOXAL-5'-PHOSPHATE
(Non-covalent)
PLP.1:
17 residues within 4Å:
Chain A:
S.100
,
G.101
,
S.102
,
N.105
,
H.129
,
Y.182
,
T.183
,
D.208
,
S.210
,
H.211
,
T.234
,
H.236
,
K.237
Chain B:
Y.54
,
G.271
,
G.272
Ligands:
SER.2
17
PLIP interactions
:
2 Ligand-Ligand interactions
,
12 interactions with chain A
,
3 interactions with chain B
Hydrogen bonds:
S.2
,
A:G.101
,
A:S.102
,
A:N.105
,
A:S.210
,
B:Y.54
,
B:G.271
,
B:G.272
Water bridges:
S.2
,
A:S.100
,
A:S.100
,
A:S.100
,
A:S.102
,
A:R.243
Salt bridges:
A:H.236
,
A:K.237
pi-Stacking:
A:H.129
PLP.4:
17 residues within 4Å:
Chain A:
Y.54
,
G.271
,
G.272
Chain B:
S.100
,
G.101
,
S.102
,
N.105
,
H.129
,
Y.182
,
T.183
,
D.208
,
S.210
,
H.211
,
T.234
,
H.236
,
K.237
Ligands:
SER.5
17
PLIP interactions
:
13 interactions with chain B
,
2 interactions with chain A
,
2 Ligand-Ligand interactions
Hydrogen bonds:
B:G.101
,
B:S.102
,
B:N.105
,
B:S.210
,
A:G.271
,
A:G.272
,
S.5
Water bridges:
B:S.100
,
B:S.100
,
B:S.100
,
B:S.102
,
B:T.232
,
B:R.243
,
S.5
Salt bridges:
B:H.236
,
B:K.237
pi-Stacking:
B:H.129
2 x
SER
:
SERINE
(Non-covalent)
SER.2:
10 residues within 4Å:
Chain A:
S.34
,
H.129
,
T.183
,
H.211
,
K.237
,
R.371
Chain B:
Y.54
,
E.56
,
Y.64
Ligands:
PLP.1
7
PLIP interactions
:
2 Ligand-Ligand interactions
,
1 interactions with chain B
,
4 interactions with chain A
Hydrogen bonds:
S.2
,
S.2
,
B:Y.64
,
A:S.34
,
A:K.237
Salt bridges:
A:H.211
,
A:R.371
SER.5:
10 residues within 4Å:
Chain A:
Y.54
,
E.56
,
Y.64
Chain B:
S.34
,
H.129
,
T.183
,
H.211
,
K.237
,
R.371
Ligands:
PLP.4
6
PLIP interactions
:
4 interactions with chain B
,
2 Ligand-Ligand interactions
Hydrogen bonds:
B:S.34
,
B:K.237
,
S.5
,
S.5
Salt bridges:
B:H.211
,
B:R.371
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.6
Ligand excluded by PLIP
CL.6:
5 residues within 4Å:
Chain A:
N.276
,
K.277
Chain B:
N.276
,
K.277
Ligands:
CL.3
Ligand excluded by PLIP
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Chitnumsub, P. et al., Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control. Acta Crystallogr.,Sect.D (2014)
Release Date
2014-12-17
Peptides
Serine hydroxymethyltransferase, putative:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
C
B
C
Export Alignment
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Secondary Structure
None
DSSP
PSIPRED
SSpro
Colour Scheme
Fade Mismatches
Enhance Mismatches
Chain
Unique Chain
Rainbow
2° Structure
Bfactor
Bfactor Range
SOA
Entropy
Clustal
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Size
Charged
Polar
Proline
Ser/Thr
Cysteine
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3D Viewer
NGL
PV
2D
FASTA
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ClustalW
PNG
Serine hydroxymethyltransferase, putative
Toggle Identical (AB)
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