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SMTL ID : 4q3b.6
(5 other biounits)
PylD cocrystallized with L-Lysine-Ne-D-lysine and NAD+
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
homo-dimer
Ligands
2 x
NAI
:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
(Non-covalent)
NAI.1:
27 residues within 4Å:
Chain A:
A.3
,
N.122
,
T.126
,
V.148
,
G.149
,
G.151
,
K.152
,
V.153
,
Y.171
,
D.172
,
A.173
,
D.174
,
L.177
,
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
,
2YF.4
,
EDO.5
16
PLIP interactions
:
16 interactions with chain A
Hydrophobic interactions:
A:T.126
,
A:V.153
,
A:P.225
Hydrogen bonds:
A:Q.123
,
A:K.152
,
A:V.153
,
A:A.173
,
A:D.174
,
A:T.205
,
A:P.225
,
A:I.227
Water bridges:
A:T.126
,
A:G.151
,
A:G.154
Salt bridges:
A:K.152
,
A:K.152
NAI.7:
26 residues within 4Å:
Chain B:
A.3
,
N.122
,
T.126
,
V.148
,
G.149
,
G.151
,
K.152
,
V.153
,
Y.171
,
D.172
,
A.173
,
D.174
,
L.177
,
A.204
,
T.205
,
P.206
,
C.207
,
T.210
,
P.225
,
G.226
,
I.227
,
E.246
,
P.247
,
L.248
Ligands:
MG.9
,
2YF.10
15
PLIP interactions
:
15 interactions with chain B
Hydrophobic interactions:
B:T.126
,
B:V.153
,
B:P.225
Hydrogen bonds:
B:K.152
,
B:V.153
,
B:G.154
,
B:A.173
,
B:D.174
,
B:T.205
,
B:T.205
,
B:I.227
,
B:E.246
Water bridges:
B:G.151
,
B:G.251
Salt bridges:
B:K.152
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.2:
7 residues within 4Å:
Chain A:
E.203
,
T.205
,
C.207
,
G.226
,
P.228
,
C.229
,
A.230
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:C.207
,
A:P.228
Water bridges:
A:T.224
NA.8:
7 residues within 4Å:
Chain B:
E.203
,
T.205
,
C.207
,
G.226
,
I.227
,
P.228
,
A.230
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:C.207
,
B:C.207
Water bridges:
B:A.230
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.9:
8 residues within 4Å:
Chain B:
Y.130
,
E.246
,
P.247
,
L.248
,
G.249
,
I.250
,
G.251
Ligands:
NAI.7
3
PLIP interactions
:
3 interactions with chain B
Metal complexes:
B:Y.130
,
B:E.246
,
B:E.246
2 x
2YF
:
N~6~-[(2R)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-L-lysine
(Non-covalent)
2YF.4:
14 residues within 4Å:
Chain A:
L.4
,
L.5
,
P.53
,
V.54
,
G.59
,
I.60
,
I.61
,
F.64
,
A.104
,
D.105
,
N.122
,
L.248
Ligands:
NAI.1
,
EDO.5
11
PLIP interactions
:
11 interactions with chain A
Hydrophobic interactions:
A:L.5
,
A:I.61
,
A:F.64
,
A:A.104
,
A:L.248
Hydrogen bonds:
A:L.5
,
A:V.54
,
A:V.54
,
A:I.61
,
A:A.104
Water bridges:
A:D.105
2YF.10:
15 residues within 4Å:
Chain B:
L.4
,
L.5
,
P.53
,
V.54
,
G.59
,
I.60
,
I.61
,
F.64
,
A.104
,
D.105
,
F.109
,
N.122
,
P.247
,
L.248
Ligands:
NAI.7
13
PLIP interactions
:
13 interactions with chain B
Hydrophobic interactions:
B:L.5
,
B:I.61
,
B:F.64
,
B:F.64
,
B:A.104
,
B:F.109
,
B:L.248
Hydrogen bonds:
B:L.5
,
B:V.54
,
B:V.54
,
B:I.61
,
B:A.104
Water bridges:
B:D.105
2 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.5:
6 residues within 4Å:
Chain A:
A.3
,
D.106
,
R.107
,
Q.123
Ligands:
NAI.1
,
2YF.4
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:R.107
,
A:Q.123
EDO.6:
2 residues within 4Å:
Chain A:
E.99
,
L.114
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:L.114
1 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.11:
8 residues within 4Å:
Chain A:
D.86
,
V.87
,
M.103
Chain B:
V.54
,
D.86
,
V.87
,
Y.90
,
M.103
2
PLIP interactions
:
1 interactions with chain B
,
1 interactions with chain A
Hydrogen bonds:
B:D.86
,
A:D.86
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
C
B
D
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PYLD, pyrrolysine synthase
Toggle Identical (AB)
Related Entries With Identical Sequence
4q39.1
|
4q39.2
|
4q39.3
|
4q39.4
|
4q3a.1
|
4q3a.2
|
4q3a.3
|
4q3a.4
|
4q3a.5
|
4q3a.6
|
4q3b.1
|
4q3b.2
|
4q3b.3
|
4q3b.4
|
4q3b.5
|
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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