Toggle navigation
Modelling
myWorkspace
Alignment Mode
User Template Mode
DeepView Project Mode
Modelling API
Template Library
Repository
SWISS-MODEL Repository
Repository API
3D-Beacons API
Annotation Projects
TBvar3D
Tools
Structure Assessment
Structure Comparison
QMEAN
Documentation
SWISS-MODEL
Examples
Video Tutorial
New Features
SWISS-MODEL Repository
QMEAN
Structure Assessment
Structure Comparison
TBvar3D
Protein Structure Course
References
Log in
Create Account
SMTL ID : 4yai.1
Crystal structure of LigL in complex with NADH and GGE from Sphingobium sp. strain SYK-6
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.60 Å
Oligo State
homo-dimer
Ligands
2 x
NAI
:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
(Non-covalent)
NAI.1:
34 residues within 4Å:
Chain A:
G.12
,
A.14
,
S.15
,
G.16
,
I.17
,
G.18
,
D.36
,
I.37
,
R.38
,
H.41
,
L.63
,
D.64
,
V.65
,
S.66
,
N.91
,
A.92
,
G.93
,
I.94
,
I.114
,
T.142
,
A.143
,
S.144
,
L.145
,
Y.158
,
K.162
,
P.188
,
G.189
,
P.190
,
I.191
,
S.193
,
R.194
,
I.195
,
N.201
,
P.203
22
PLIP interactions
:
22 interactions with chain A
Hydrophobic interactions:
A:P.188
Hydrogen bonds:
A:S.15
,
A:I.17
,
A:D.36
,
A:I.37
,
A:H.41
,
A:D.64
,
A:V.65
,
A:A.92
,
A:Y.158
,
A:K.162
,
A:I.191
,
A:I.191
,
A:S.193
,
A:S.193
,
A:R.194
,
A:N.201
Water bridges:
A:G.18
,
A:N.91
,
A:S.193
,
A:N.201
,
A:N.201
NAI.3:
35 residues within 4Å:
Chain B:
G.12
,
A.14
,
S.15
,
G.16
,
I.17
,
G.18
,
D.36
,
I.37
,
R.38
,
H.41
,
L.63
,
D.64
,
V.65
,
S.66
,
N.91
,
A.92
,
G.93
,
I.94
,
I.114
,
T.142
,
A.143
,
S.144
,
L.145
,
Y.158
,
K.162
,
P.188
,
G.189
,
P.190
,
I.191
,
S.193
,
R.194
,
I.195
,
N.201
,
P.203
Ligands:
GGE.4
23
PLIP interactions
:
23 interactions with chain B
Hydrophobic interactions:
B:P.188
Hydrogen bonds:
B:S.15
,
B:I.17
,
B:D.36
,
B:I.37
,
B:R.38
,
B:H.41
,
B:D.64
,
B:V.65
,
B:A.92
,
B:Y.158
,
B:K.162
,
B:I.191
,
B:I.191
,
B:S.193
,
B:S.193
,
B:R.194
,
B:N.201
Water bridges:
B:G.18
,
B:N.91
,
B:S.193
,
B:N.201
,
B:N.201
1 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
1 residues within 4Å:
Chain A:
E.77
No protein-ligand interaction detected (PLIP)
1 x
GGE
:
(1S,2R)-1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol
(Non-covalent)
GGE.4:
19 residues within 4Å:
Chain B:
D.95
,
S.97
,
S.144
,
L.145
,
A.146
,
T.149
,
M.151
,
M.155
,
Y.158
,
P.188
,
G.189
,
P.190
,
I.191
,
I.195
,
L.219
,
R.222
,
W.228
,
W.255
Ligands:
NAI.3
11
PLIP interactions
:
11 interactions with chain B
Hydrophobic interactions:
B:A.146
,
B:T.149
,
B:Y.158
,
B:W.255
Hydrogen bonds:
B:D.95
,
B:S.144
,
B:S.144
,
B:S.144
,
B:L.145
,
B:R.222
,
B:R.222
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Pereira, J.H. et al., Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. J.Biol.Chem. (2016)
Release Date
2016-03-09
Peptides
C alpha-dehydrogenase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
Export Alignment
FASTA format
Clustal Format
PNG Image
Secondary Structure
None
DSSP
PSIPRED
SSpro
Colour Scheme
Fade Mismatches
Enhance Mismatches
Chain
Unique Chain
Rainbow
2° Structure
Bfactor
Bfactor Range
SOA
Entropy
Clustal
Hydrophobic
Size
Charged
Polar
Proline
Ser/Thr
Cysteine
Aliphatic
Aromatic
No Colour
Background
3D Viewer
NGL
PV
2D
FASTA
Multi FASTA
ClustalW
PNG
C alpha-dehydrogenase
Toggle Identical (AB)
Related Entries With Identical Sequence
4yae.1
|
4yag.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
Low
Medium
High
Extreme