SMTL ID : 7xrd.1

Cryo-EM structure of Arf6 helical polymer assembled on lipid membrane

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.26, D.62 Ligands: GTP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.26, A:D.62, A:D.62 MG.3: 3 residues within 4Å: Chain B: D.21, P.42 Ligands: GTP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.21, B:D.21 MG.5: 2 residues within 4Å: Chain C: D.21 Ligands: GTP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.21, C:D.21 MG.7: 3 residues within 4Å: Chain D: T.26, D.62 Ligands: GTP.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.26, D:D.62, D:D.62

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)(Covalent)

GTP.2: 16 residues within 4Å: Chain A: L.20, A.23, G.24, K.25, T.26, T.27, T.40, P.42, T.43, G.65, N.121, K.122, C.154, A.155, T.156 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.22, A:A.23, A:G.24, A:K.25, A:T.26, A:T.27, A:T.27, A:T.43, A:T.43, A:G.65, A:N.121, A:K.122, A:A.155, A:T.156, A:T.156 Salt bridges: A:K.25, A:D.124 GTP.4: 17 residues within 4Å: Chain B: D.21, A.22, G.24, T.26, T.27, T.40, I.41, P.42, T.43, Q.66, N.121, K.122, D.124, C.154, A.155, T.156 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:A.22, B:G.24, B:T.26, B:T.26, B:T.27, B:T.27, B:T.43, B:T.43, B:T.43, B:Q.66, B:N.121, B:A.155, B:T.156, B:T.156 Salt bridges: B:K.25, B:D.124 GTP.6: 19 residues within 4Å: Chain C: D.21, A.23, G.24, K.25, T.26, T.27, T.40, P.42, T.43, G.65, Q.66, N.121, K.122, D.124, L.125, C.154, A.155, T.156 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:A.23, C:G.24, C:K.25, C:T.26, C:T.26, C:T.40, C:T.43, C:G.65, C:Q.66, C:N.121, C:K.122, C:A.155, C:T.156 Salt bridges: C:K.25, C:K.25, C:D.124 GTP.8: 17 residues within 4Å: Chain D: A.22, G.24, K.25, T.26, T.27, T.40, I.41, P.42, T.43, G.64, Q.66, N.121, K.122, C.154, A.155, T.156 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:A.22, D:G.24, D:T.27, D:T.40, D:T.43, D:N.121, D:K.122, D:A.155, D:T.156, D:T.156 Salt bridges: D:D.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, X.Y. et al., Cryo-EM structure of Arf6 helical polymer assembled on lipid membrane. To Be Published

Release Date

2023-11-15

Peptides

ADP-ribosylation factor 6: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ADP-ribosylation factor 6