SMTL ID : 6vjf.1 (1 other biounit)

The P-Loop K to A mutation of C. therm Vps1 GTPase-BSE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-dimer

Ligands

2 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.1: 26 residues within 4Å: Chain A: Q.54, S.55, S.56, G.57, A.58, S.59, S.60, R.73, G.74, Q.75, 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 23 PLIP interactions: 22 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:T.79, A:G.175, A:K.242, A:K.242, A:N.272 Water bridges: A:S.59, A:P.72, A:T.79, A:L.173 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 22 PLIP interactions: 21 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:G.175, B:K.242, B:K.242, B:N.272, B:N.272 Water bridges: B:P.72, B:T.79, B:T.79 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, H2O.1, H2O.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, H2O.1, H2O.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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative sorting protein Vps1

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