SMTL ID : 6dlu.1

Cryo-EM of the GMPPCP-bound human dynamin-1 polymer assembled on the membrane in the constricted state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

GCP.1: 23 residues within 4Å: Chain A: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, I.63, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain B: D.211 Ligands: MG.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.41, A:A.42, A:G.43, A:K.44, A:K.44, A:S.45, A:S.46, A:G.60, A:V.64, A:T.65, A:T.65, A:G.139, A:K.206, A:K.206, A:N.236, A:N.236 Salt bridges: A:D.208, B:D.211 GCP.3: 23 residues within 4Å: Chain A: D.211 Chain B: Q.40, S.41, G.43, K.44, S.45, S.46, R.59, G.60, I.63, V.64, T.65, G.139, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: MG.4 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.41, B:A.42, B:G.43, B:K.44, B:S.45, B:S.46, B:G.60, B:V.64, B:T.65, B:T.65, B:G.139, B:K.206, B:K.206, B:N.236, B:N.236, B:S.238, B:Q.239 Salt bridges: B:K.44, B:D.208, A:D.211

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.45, T.65 Ligands: GCP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.45, A:T.65 MG.4: 5 residues within 4Å: Chain B: S.45, P.58, T.65, D.136 Ligands: GCP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.45, B:T.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kong, L. et al., Cryo-EM of the dynamin polymer assembled on lipid membrane. Nature (2018)

Release Date

2018-08-01

Peptides

Dynamin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
P

Dynamin-1

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