SMTL ID : 6djq.2 (1 other biounit)

Vps1 GTPase-BSE fusion complexed with GDP.AlF4-

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 24 residues within 4Å: Chain A: S.55, S.56, G.57, K.58, S.59, S.60, R.73, G.74, Q.75, T.241, K.242, D.244, L.245, V.270, V.271, N.272, R.273, G.274, Q.275, I.278 Chain B: D.247 Ligands: ALF.2, MG.3, NA.4 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.53, A:S.55, A:S.56, A:S.56, A:G.57, A:K.58, A:S.59, A:S.60, A:S.60, A:G.74, A:K.242, A:K.242, A:N.272, A:N.272, A:R.273 Water bridges: A:T.79 Salt bridges: A:K.58, A:D.244, B:D.247 GDP.5: 24 residues within 4Å: Chain A: D.247 Chain B: S.55, S.56, G.57, K.58, S.59, S.60, R.73, G.74, Q.75, T.241, K.242, D.244, L.245, V.270, V.271, N.272, R.273, G.274, Q.275, I.278 Ligands: ALF.6, MG.7, NA.8 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.55, B:S.56, B:G.57, B:K.58, B:S.59, B:S.59, B:S.60, B:S.60, B:G.74, B:T.79, B:K.242, B:K.242, B:N.272, B:N.272, B:R.273, A:D.247 Water bridges: B:S.59, B:G.175 Salt bridges: B:K.58, B:D.244, A:D.247

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 13 residues within 4Å: Chain A: Q.54, S.55, K.58, G.74, G.76, I.77, V.78, T.79, P.174, G.175 Ligands: GDP.1, MG.3, NA.4 No protein-ligand interaction detected (PLIP) ALF.6: 14 residues within 4Å: Chain B: Q.54, S.55, K.58, S.59, G.76, I.77, V.78, T.79, L.173, P.174, G.175 Ligands: GDP.5, MG.7, NA.8 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.59, T.79 Ligands: GDP.1, ALF.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.59, A:T.79, H2O.1 MG.7: 6 residues within 4Å: Chain B: K.58, S.59, T.79, D.172 Ligands: GDP.5, ALF.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.59, B:T.79, H2O.1, H2O.1

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 8 residues within 4Å: Chain A: S.55, G.74, Q.75, G.76, I.77, V.78 Ligands: GDP.1, ALF.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.55, A:Q.75, A:V.78 NA.8: 9 residues within 4Å: Chain B: Q.54, S.55, G.74, Q.75, G.76, I.77, V.78 Ligands: GDP.5, ALF.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.55, B:V.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varlakhanova, N.V. et al., Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture. J. Cell Biol. (2018)

Release Date

2018-08-22

Peptides

Vps1 GTPase-BSE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Vps1 GTPase-BSE

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