SMTL ID : 8r1a.1

Model of the membrane-bound GBP1 oligomer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.1: 11 residues within 4Å: Chain A: L.57, Y.58, R.59, K.62, S.63, S.84, H.85, T.86, G.111 Ligands: MG.2, GDP.3 No protein-ligand interaction detected (PLIP) AF3.4: 11 residues within 4Å: Chain B: L.57, Y.58, R.59, K.62, S.63, S.84, H.85, T.86, G.111 Ligands: MG.5, GDP.6 No protein-ligand interaction detected (PLIP) AF3.7: 11 residues within 4Å: Chain C: L.57, Y.58, R.59, K.62, S.63, S.84, H.85, T.86, G.111 Ligands: MG.8, GDP.9 No protein-ligand interaction detected (PLIP) AF3.10: 11 residues within 4Å: Chain D: L.57, Y.58, R.59, K.62, S.63, S.84, H.85, T.86, G.111 Ligands: MG.11, GDP.12 No protein-ligand interaction detected (PLIP) AF3.13: 11 residues within 4Å: Chain E: L.57, Y.58, R.59, K.62, S.63, S.84, H.85, T.86, G.111 Ligands: MG.14, GDP.15 No protein-ligand interaction detected (PLIP) AF3.16: 11 residues within 4Å: Chain F: L.57, Y.58, R.59, K.62, S.63, S.84, H.85, T.86, G.111 Ligands: MG.17, GDP.18 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.63, S.77, T.86 Ligands: AF3.1, GDP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.63, A:T.86 MG.5: 5 residues within 4Å: Chain B: S.63, S.77, T.86 Ligands: AF3.4, GDP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.63, B:T.86 MG.8: 5 residues within 4Å: Chain C: S.63, S.77, T.86 Ligands: AF3.7, GDP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.63, C:T.86 MG.11: 5 residues within 4Å: Chain D: S.63, S.77, T.86 Ligands: AF3.10, GDP.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.63, D:T.86 MG.14: 5 residues within 4Å: Chain E: S.63, S.77, T.86 Ligands: AF3.13, GDP.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.63, E:T.86 MG.17: 5 residues within 4Å: Chain F: S.63, S.77, T.86 Ligands: AF3.16, GDP.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.63, F:T.86

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

GDP.3: 19 residues within 4Å: Chain A: R.59, T.60, G.61, K.62, S.63, Y.64, L.78, G.79, S.80, R.194, D.195, P.252, L.258, A.259, L.261, F.273 Chain B: R.251 Ligands: AF3.1, MG.2 18 PLIP interactions: 1 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:R.251, A:R.59, A:T.60, A:G.61, A:K.62, A:S.63, A:S.63, A:Y.64, A:G.79, A:G.79, A:T.86, A:T.86, A:R.194, A:L.261 Salt bridges: A:R.59, A:R.59, A:K.62, A:D.195 GDP.6: 18 residues within 4Å: Chain A: R.251 Chain B: R.59, T.60, G.61, K.62, S.63, Y.64, L.78, G.79, S.80, T.86, R.194, D.195, P.252, L.258, L.261 Ligands: AF3.4, MG.5 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.59, B:T.60, B:G.61, B:K.62, B:S.63, B:S.63, B:Y.64, B:G.79, B:G.79, B:T.86, B:R.194, A:R.251, A:R.251 Salt bridges: B:R.59, B:R.59, B:K.62, B:D.195 GDP.9: 19 residues within 4Å: Chain C: R.59, T.60, G.61, K.62, S.63, Y.64, L.78, G.79, S.80, R.194, D.195, P.252, L.258, A.259, L.261, F.273 Chain D: R.251 Ligands: AF3.7, MG.8 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.59, C:T.60, C:G.61, C:K.62, C:S.63, C:S.63, C:Y.64, C:G.79, C:G.79, C:T.86, C:T.86, C:R.194, C:L.261, D:R.251 Salt bridges: C:R.59, C:R.59, C:K.62, C:D.195 GDP.12: 18 residues within 4Å: Chain C: R.251 Chain D: R.59, T.60, G.61, K.62, S.63, Y.64, L.78, G.79, S.80, T.86, R.194, D.195, P.252, L.258, L.261 Ligands: AF3.10, MG.11 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.59, D:T.60, D:G.61, D:K.62, D:S.63, D:S.63, D:Y.64, D:G.79, D:G.79, D:T.86, D:R.194, C:R.251, C:R.251 Salt bridges: D:R.59, D:R.59, D:K.62, D:D.195 GDP.15: 19 residues within 4Å: Chain E: R.59, T.60, G.61, K.62, S.63, Y.64, L.78, G.79, S.80, R.194, D.195, P.252, L.258, A.259, L.261, F.273 Chain F: R.251 Ligands: AF3.13, MG.14 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.59, E:T.60, E:G.61, E:K.62, E:S.63, E:S.63, E:Y.64, E:G.79, E:G.79, E:T.86, E:T.86, E:R.194, E:L.261, F:R.251 Salt bridges: E:R.59, E:R.59, E:K.62, E:D.195 GDP.18: 18 residues within 4Å: Chain E: R.251 Chain F: R.59, T.60, G.61, K.62, S.63, Y.64, L.78, G.79, S.80, T.86, R.194, D.195, P.252, L.258, L.261 Ligands: AF3.16, MG.17 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.59, F:T.60, F:G.61, F:K.62, F:S.63, F:S.63, F:Y.64, F:G.79, F:G.79, F:T.86, F:R.194, E:R.251, E:R.251 Salt bridges: F:R.59, F:R.59, F:K.62, F:D.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weismehl, M. et al., Structural insights into the activation mechanism of antimicrobial GBP1. Embo J. (2024)

Release Date

2024-01-17

Peptides

Guanylate binding protein 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Guanylate binding protein 1