SMTL ID : 8cqb.1

Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

GDP.1: 17 residues within 4Å: Chain A: R.48, T.49, G.50, K.51, S.52, Y.53, L.67, G.68, S.69, T.75, R.183, D.184, P.241, L.247, L.250 Ligands: AF3.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.48, A:T.49, A:G.50, A:K.51, A:S.52, A:Y.53, A:G.68, A:G.100, A:R.183 Salt bridges: A:R.48, A:R.48, A:D.184 GDP.4: 17 residues within 4Å: Chain B: R.48, G.50, K.51, S.52, Y.53, L.67, G.68, S.69, T.75, I.131, R.183, D.184, P.241, L.247, L.250 Ligands: AF3.5, MG.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.48, B:G.50, B:K.51, B:S.52, B:G.68, B:T.75, B:R.183 Salt bridges: B:R.48, B:R.48, B:K.51, B:D.184

2 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.2: 9 residues within 4Å: Chain A: Y.47, K.51, S.73, H.74, T.75, E.99, G.100 Ligands: GDP.1, MG.3 No protein-ligand interaction detected (PLIP) AF3.5: 11 residues within 4Å: Chain B: R.48, K.51, S.52, S.73, H.74, T.75, T.98, E.99, G.100 Ligands: GDP.4, MG.6 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.52, T.75, D.97 Ligands: GDP.1, AF3.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.52, A:T.75 MG.6: 5 residues within 4Å: Chain B: S.52, T.75, D.97 Ligands: GDP.4, AF3.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.52, B:T.75, B:D.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhm, T.I. et al., Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3. To Be Published

Release Date

2024-03-13

Peptides

Guanylate-binding protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Guanylate-binding protein 1