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SMTL ID : 4v7n.5
(17 other biounits)
Glycocyamine kinase, beta-beta homodimer from marine worm Namalycastis sp., with transition state analog Mg(II)-ADP-NO3-glycocyamine.
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.30 Å
Oligo State
homo-dimer
Ligands
2 x
NMG
:
GUANIDINO ACETATE
(Non-covalent)
NMG.1:
9 residues within 4Å:
Chain A:
K.83
,
T.84
,
L.212
,
E.243
,
C.294
,
T.296
,
N.297
,
E.336
Ligands:
NO3.4
10
PLIP interactions
:
10 interactions with chain A
Hydrogen bonds:
A:T.84
,
A:T.84
,
A:T.296
,
A:T.296
,
A:N.297
Water bridges:
A:G.85
,
A:E.336
Salt bridges:
A:K.83
,
A:E.243
,
A:E.336
NMG.5:
8 residues within 4Å:
Chain B:
K.83
,
T.84
,
L.212
,
E.243
,
C.294
,
T.296
,
E.336
Ligands:
NO3.8
8
PLIP interactions
:
8 interactions with chain B
Hydrogen bonds:
B:K.83
,
B:T.84
,
B:T.84
,
B:E.336
Water bridges:
B:R.331
Salt bridges:
B:K.83
,
B:E.243
,
B:E.336
2 x
ADP
:
ADENOSINE-5'-DIPHOSPHATE
(Non-covalent)
ADP.2:
19 residues within 4Å:
Chain A:
S.139
,
C.140
,
R.141
,
R.143
,
H.202
,
W.239
,
R.247
,
R.303
,
S.305
,
V.306
,
H.307
,
R.331
,
T.333
,
G.334
,
G.335
,
E.336
,
D.346
Ligands:
MG.3
,
NO3.4
17
PLIP interactions
:
17 interactions with chain A
Hydrogen bonds:
A:S.139
,
A:R.303
,
A:S.305
,
A:G.334
,
A:E.336
Water bridges:
A:R.141
,
A:R.141
,
A:R.247
,
A:R.247
Salt bridges:
A:R.141
,
A:R.143
,
A:R.247
,
A:R.303
,
A:R.303
,
A:R.331
,
A:R.331
pi-Stacking:
A:H.307
ADP.6:
19 residues within 4Å:
Chain B:
S.139
,
R.141
,
R.143
,
H.202
,
W.239
,
R.247
,
M.251
,
R.303
,
S.305
,
V.306
,
H.307
,
R.331
,
T.333
,
G.334
,
G.335
,
E.336
,
D.346
Ligands:
MG.7
,
NO3.8
23
PLIP interactions
:
23 interactions with chain B
Hydrogen bonds:
B:S.139
,
B:H.202
,
B:R.303
,
B:S.305
,
B:T.333
,
B:E.336
,
B:D.346
Water bridges:
B:R.141
,
B:R.141
,
B:R.141
,
B:L.204
,
B:R.247
,
B:G.335
,
B:E.336
,
B:S.337
Salt bridges:
B:R.141
,
B:R.143
,
B:R.247
,
B:R.303
,
B:R.303
,
B:R.331
,
B:R.331
pi-Stacking:
B:H.307
2 x
MG
:
MAGNESIUM ION
(Non-functional Binders)
MG.3:
2 residues within 4Å:
Ligands:
ADP.2
,
NO3.4
No protein-ligand interaction detected (PLIP)
MG.7:
2 residues within 4Å:
Ligands:
ADP.6
,
NO3.8
No protein-ligand interaction detected (PLIP)
2 x
NO3
:
NITRATE ION
(Non-functional Binders)
NO3.4:
8 residues within 4Å:
Chain A:
R.143
,
E.243
,
R.247
,
R.331
,
E.336
Ligands:
NMG.1
,
ADP.2
,
MG.3
8
PLIP interactions
:
8 interactions with chain A
Hydrogen bonds:
A:R.143
,
A:R.247
,
A:R.247
,
A:R.331
,
A:R.331
Water bridges:
A:E.243
,
A:N.297
,
A:E.336
NO3.8:
8 residues within 4Å:
Chain B:
R.143
,
E.243
,
R.247
,
R.331
,
E.336
Ligands:
NMG.5
,
ADP.6
,
MG.7
7
PLIP interactions
:
7 interactions with chain B
Hydrogen bonds:
B:R.143
,
B:R.247
,
B:R.247
,
B:R.331
,
B:R.331
,
B:E.336
Water bridges:
B:E.336
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Lim, K. et al., Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member. Biochemistry (2010)
Release Date
2014-07-09
Peptides
Glycocyamine kinase beta chain:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
AI
B
AJ
Export Alignment
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Secondary Structure
None
DSSP
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Colour Scheme
Fade Mismatches
Enhance Mismatches
Chain
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Rainbow
2° Structure
Bfactor
Bfactor Range
SOA
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Glycocyamine kinase beta chain
Related Entries With Identical Sequence
3l2d.1
|
3l2d.2
|
3l2d.3
|
3l2d.4
|
3l2e.1
|
3l2e.2
|
3l2e.4
|
3l2e.6
|
4v7n.1
|
4v7n.2
|
4v7n.3
|
4v7n.4
|
4v7n.6
|
4v7n.7
|
4v7n.8
|
4v7n.9
|
4v7n.10
|
4v7n.11
|
4v7n.12
|
4v7n.13
|
4v7n.14
|
4v7n.15
|
4v7n.16
|
4v7n.17
|
4v7n.18
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
Low
Medium
High
Extreme