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SMTL ID : 6vjf.2
(1 other biounit)
The P-Loop K to A mutation of C. therm Vps1 GTPase-BSE
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.47 Å
Oligo State
homo-dimer
Ligands
2 x
GCP
:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
(Non-covalent)
GCP.1:
25 residues within 4Å:
Chain A:
Q.54
,
S.55
,
S.56
,
G.57
,
A.58
,
S.59
,
S.60
,
R.73
,
G.74
,
G.76
,
I.77
,
V.78
,
T.79
,
G.175
,
K.242
,
D.244
,
L.245
,
V.271
,
N.272
,
R.273
,
G.274
,
Q.275
,
I.278
Chain B:
D.247
Ligands:
MG.2
24
PLIP interactions
:
23 interactions with chain A
,
1 interactions with chain B
Hydrogen bonds:
A:Q.54
,
A:S.55
,
A:G.57
,
A:A.58
,
A:S.59
,
A:S.60
,
A:S.60
,
A:G.74
,
A:G.74
,
A:V.78
,
A:T.79
,
A:G.175
,
A:K.242
,
A:K.242
,
A:N.272
,
A:N.272
Water bridges:
A:P.72
,
A:T.79
,
A:T.79
,
A:D.244
,
A:G.274
Salt bridges:
A:D.244
,
B:D.247
pi-Cation interactions:
A:K.242
GCP.3:
25 residues within 4Å:
Chain A:
D.247
Chain B:
Q.54
,
S.55
,
S.56
,
G.57
,
A.58
,
S.59
,
S.60
,
R.73
,
G.74
,
G.76
,
I.77
,
V.78
,
T.79
,
G.175
,
K.242
,
D.244
,
L.245
,
V.271
,
N.272
,
R.273
,
G.274
,
Q.275
,
I.278
Ligands:
MG.4
24
PLIP interactions
:
23 interactions with chain B
,
1 interactions with chain A
Hydrogen bonds:
B:Q.54
,
B:S.55
,
B:G.57
,
B:A.58
,
B:S.59
,
B:S.60
,
B:S.60
,
B:G.74
,
B:G.74
,
B:V.78
,
B:T.79
,
B:T.79
,
B:T.79
,
B:G.175
,
B:K.242
,
B:K.242
,
B:N.272
,
B:N.272
,
B:Q.275
Water bridges:
B:S.59
,
B:P.72
Salt bridges:
B:D.244
,
A:D.247
pi-Cation interactions:
B:K.242
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.2:
4 residues within 4Å:
Chain A:
S.59
,
T.79
,
D.172
Ligands:
GCP.1
4
PLIP interactions
:
2 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:S.59
,
A:T.79
,
H
2
O.1
,
H
2
O.1
MG.4:
4 residues within 4Å:
Chain B:
S.59
,
T.79
,
D.172
Ligands:
GCP.3
4
PLIP interactions
:
2 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:S.59
,
B:T.79
,
H
2
O.1
,
H
2
O.1
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Tornabene, B.A. et al., Structural and functional characterization of the dominant negative P-loop lysine mutation in the dynamin superfamily protein Vps1. Protein Sci. (2020)
Release Date
2020-02-19
Peptides
Putative sorting protein Vps1:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
C
B
D
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Putative sorting protein Vps1
Related Entries With Identical Sequence
6vjf.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
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