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 : 4ckl.1
(1 other biounit)
Structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit with simocyclinone D8 bound
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.05 Å
Oligo State
homo-dimer
Ligands
2 x
SM8
:
SIMOCYCLINONE D8
(Non-covalent)
SM8.1:
24 residues within 4Å:
Chain A:
K.13
,
V.15
,
H.16
,
H.49
,
P.50
,
H.51
,
G.52
,
D.53
,
A.55
,
R.62
,
L.69
,
N.140
,
G.141
,
S.142
,
S.143
,
Y.237
Chain B:
I.45
,
G.52
,
D.53
,
S.54
,
Y.57
,
A.90
,
M.91
,
R.92
19
PLIP interactions
:
12 interactions with chain A
,
7 interactions with chain B
Hydrophobic interactions:
A:V.15
,
A:H.51
,
A:D.53
,
A:A.55
,
B:I.45
,
B:Y.57
Hydrogen bonds:
A:H.51
,
A:G.52
,
A:S.143
,
A:S.143
,
B:M.91
,
B:R.92
Salt bridges:
A:H.16
,
A:H.49
,
A:H.51
,
A:R.62
Water bridges:
B:S.54
,
B:Y.57
,
B:R.92
SM8.2:
24 residues within 4Å:
Chain A:
I.45
,
G.52
,
D.53
,
S.54
,
Y.57
,
A.90
,
M.91
,
R.92
Chain B:
K.13
,
V.15
,
H.16
,
H.49
,
P.50
,
H.51
,
G.52
,
D.53
,
A.55
,
R.62
,
L.69
,
N.140
,
G.141
,
S.142
,
S.143
,
Y.237
20
PLIP interactions
:
7 interactions with chain A
,
13 interactions with chain B
Hydrophobic interactions:
A:I.45
,
A:Y.57
,
B:V.15
,
B:H.51
,
B:D.53
,
B:A.55
Hydrogen bonds:
A:M.91
,
A:R.92
,
B:H.51
,
B:G.52
,
B:S.143
,
B:S.143
Water bridges:
A:S.54
,
A:Y.57
,
A:R.92
,
B:D.53
Salt bridges:
B:H.16
,
B:H.49
,
B:H.51
,
B:R.62
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Hearnshaw, S.J. et al., A New Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8 Bound to DNA Gyrase Gives Fresh Insight Into the Mechanism of Inhibition. J.Mol.Biol. (2014)
Release Date
2014-03-12
Peptides
DNA GYRASE SUBUNIT A:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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
DNA GYRASE SUBUNIT A
Toggle Identical (AB)
Related Entries With Identical Sequence
1ab4.1
|
4ckk.1
|
4ckk.2
|
4ckl.2
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
Low
Medium
High
Extreme