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SMTL ID : 4q39.4
(3 other biounits)
PylD in complex with pyrrolysine and NADH
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.20 Å
Oligo State
homo-dimer
Ligands
2 x
NAI
:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
(Non-covalent)
NAI.1:
26 residues within 4Å:
Chain A:
A.3
,
N.122
,
Q.123
,
T.126
,
V.148
,
G.149
,
G.151
,
K.152
,
V.153
,
Y.171
,
D.172
,
A.173
,
D.174
,
A.204
,
T.205
,
P.206
,
C.207
,
T.210
,
P.225
,
G.226
,
I.227
,
E.246
,
P.247
,
L.248
Ligands:
MG.3
,
PYL.4
18
PLIP interactions
:
18 interactions with chain A
Hydrophobic interactions:
A:T.126
,
A:V.153
,
A:P.225
Hydrogen bonds:
A:A.3
,
A:Q.123
,
A:G.151
,
A:K.152
,
A:V.153
,
A:G.154
,
A:A.173
,
A:D.174
,
A:T.205
,
A:P.225
,
A:I.227
Water bridges:
A:N.122
,
A:T.210
Salt bridges:
A:K.152
,
A:K.152
NAI.6:
26 residues within 4Å:
Chain B:
A.3
,
N.122
,
Q.123
,
T.126
,
V.148
,
G.149
,
G.151
,
K.152
,
V.153
,
Y.171
,
D.172
,
A.173
,
D.174
,
A.204
,
T.205
,
P.206
,
C.207
,
T.210
,
P.225
,
G.226
,
I.227
,
E.246
,
P.247
,
L.248
Ligands:
MG.8
,
PYL.9
18
PLIP interactions
:
18 interactions with chain B
Hydrophobic interactions:
B:T.126
,
B:V.153
,
B:P.225
Hydrogen bonds:
B:A.3
,
B:Q.123
,
B:G.151
,
B:K.152
,
B:V.153
,
B:G.154
,
B:A.173
,
B:D.174
,
B:T.205
,
B:P.225
,
B:I.227
Water bridges:
B:N.122
,
B:T.210
Salt bridges:
B:K.152
,
B:K.152
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.2:
8 residues within 4Å:
Chain A:
E.203
,
T.205
,
C.207
,
G.226
,
I.227
,
P.228
,
C.229
,
A.230
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:T.205
,
A:T.205
,
A:C.207
Water bridges:
A:A.230
NA.7:
8 residues within 4Å:
Chain B:
E.203
,
T.205
,
C.207
,
G.226
,
I.227
,
P.228
,
C.229
,
A.230
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:T.205
,
B:C.207
Water bridges:
B:T.224
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.3:
7 residues within 4Å:
Chain A:
Y.130
,
E.246
,
L.248
,
G.249
,
I.250
,
G.251
Ligands:
NAI.1
3
PLIP interactions
:
3 interactions with chain A
Metal complexes:
A:Y.130
,
A:E.246
,
A:E.246
MG.8:
7 residues within 4Å:
Chain B:
Y.130
,
E.246
,
L.248
,
G.249
,
I.250
,
G.251
Ligands:
NAI.6
3
PLIP interactions
:
3 interactions with chain B
Metal complexes:
B:Y.130
,
B:E.246
,
B:E.246
2 x
PYL
:
PYRROLYSINE
(Non-covalent)
PYL.4:
14 residues within 4Å:
Chain A:
A.3
,
L.4
,
L.5
,
P.53
,
V.54
,
G.59
,
I.60
,
I.61
,
F.64
,
A.104
,
D.105
,
F.109
,
N.122
Ligands:
NAI.1
11
PLIP interactions
:
11 interactions with chain A
Hydrophobic interactions:
A:L.5
,
A:I.61
,
A:F.64
,
A:F.109
Hydrogen bonds:
A:L.5
,
A:V.54
,
A:I.61
,
A:I.61
,
A:A.104
Water bridges:
A:S.65
,
A:D.105
PYL.9:
14 residues within 4Å:
Chain B:
A.3
,
L.4
,
L.5
,
P.53
,
V.54
,
G.59
,
I.60
,
I.61
,
F.64
,
A.104
,
D.105
,
F.109
,
N.122
Ligands:
NAI.6
11
PLIP interactions
:
11 interactions with chain B
Hydrophobic interactions:
B:L.5
,
B:I.61
,
B:F.64
,
B:F.109
Hydrogen bonds:
B:L.5
,
B:V.54
,
B:I.61
,
B:I.61
,
B:A.104
Water bridges:
B:S.65
,
B:D.105
2 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.5:
4 residues within 4Å:
Chain A:
A.20
,
L.243
,
I.244
,
A.245
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:A.245
EDO.10:
4 residues within 4Å:
Chain B:
A.20
,
L.243
,
I.244
,
A.245
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:A.245
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Quitterer, F. et al., The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD). Angew.Chem.Int.Ed.Engl. (2014)
Release Date
2014-04-23
Peptides
PYLD, pyrrolysine synthase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
B
B
B
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Secondary Structure
None
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Colour Scheme
Fade Mismatches
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2° Structure
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PYLD, pyrrolysine synthase
Toggle Identical (AB)
Related Entries With Identical Sequence
4q39.1
|
4q39.2
|
4q39.3
|
4q3a.1
|
4q3a.2
|
4q3a.3
|
4q3a.4
|
4q3a.5
|
4q3a.6
|
4q3b.1
|
4q3b.2
|
4q3b.3
|
4q3b.4
|
4q3b.5
|
4q3b.6
|
4q3c.1
|
4q3c.2
|
4q3c.3
|
4q3c.4
|
4q3c.5
|
4q3c.6
|
4q3d.1
|
4q3d.2
|
4q3d.3
|
4q3d.4
|
4q3d.5
|
4q3d.6
|
4q3e.1
|
4q3e.2
|
4q3e.3
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