SMTL ID : 5wp9.1

Structural Basis of Mitochondrial Receptor Binding and Constriction by Dynamin-Related Protein 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-mer

Ligands

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

GCP.1: 28 residues within 4Å: Chain A: Q.34, S.35, S.36, G.37, K.38, S.39, S.40, R.53, G.54, T.55, G.56, I.57, V.58, T.59, P.148, G.149, T.215, K.216, D.218, L.219, V.244, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.35, A:S.36, A:G.37, A:K.38, A:K.38, A:S.39, A:S.40, A:S.40, A:G.54, A:G.54, A:V.58, A:T.59, A:G.149, A:K.216, A:K.216, A:N.246, A:Q.249 Salt bridges: A:D.218 GCP.3: 28 residues within 4Å: Chain C: Q.34, S.35, S.36, G.37, K.38, S.39, S.40, R.53, G.54, T.55, G.56, I.57, V.58, T.59, P.148, G.149, T.215, K.216, D.218, L.219, V.244, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:S.35, C:S.36, C:G.37, C:K.38, C:K.38, C:S.39, C:S.40, C:S.40, C:G.54, C:G.54, C:V.58, C:T.59, C:G.149, C:K.216, C:K.216, C:N.246, C:Q.249 Salt bridges: C:D.218 GCP.5: 28 residues within 4Å: Chain E: Q.34, S.35, S.36, G.37, K.38, S.39, S.40, R.53, G.54, T.55, G.56, I.57, V.58, T.59, P.148, G.149, T.215, K.216, D.218, L.219, V.244, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:S.35, E:S.36, E:G.37, E:K.38, E:K.38, E:S.39, E:S.40, E:S.40, E:G.54, E:G.54, E:V.58, E:T.59, E:G.149, E:K.216, E:K.216, E:N.246, E:Q.249 Salt bridges: E:D.218 GCP.7: 28 residues within 4Å: Chain G: Q.34, S.35, S.36, G.37, K.38, S.39, S.40, R.53, G.54, T.55, G.56, I.57, V.58, T.59, P.148, G.149, T.215, K.216, D.218, L.219, V.244, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.8 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:S.35, G:S.36, G:G.37, G:K.38, G:K.38, G:S.39, G:S.40, G:S.40, G:G.54, G:G.54, G:V.58, G:T.59, G:G.149, G:K.216, G:K.216, G:N.246, G:Q.249 Salt bridges: G:D.218 GCP.9: 28 residues within 4Å: Chain I: Q.34, S.35, S.36, G.37, K.38, S.39, S.40, R.53, G.54, T.55, G.56, I.57, V.58, T.59, P.148, G.149, T.215, K.216, D.218, L.219, V.244, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.10 18 PLIP interactions: 18 interactions with chain I Hydrogen bonds: I:S.35, I:S.36, I:G.37, I:K.38, I:K.38, I:S.39, I:S.40, I:S.40, I:G.54, I:G.54, I:V.58, I:T.59, I:G.149, I:K.216, I:K.216, I:N.246, I:Q.249 Salt bridges: I:D.218 GCP.11: 28 residues within 4Å: Chain K: Q.34, S.35, S.36, G.37, K.38, S.39, S.40, R.53, G.54, T.55, G.56, I.57, V.58, T.59, P.148, G.149, T.215, K.216, D.218, L.219, V.244, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.12 18 PLIP interactions: 18 interactions with chain K Hydrogen bonds: K:S.35, K:S.36, K:G.37, K:K.38, K:K.38, K:S.39, K:S.40, K:S.40, K:G.54, K:G.54, K:V.58, K:T.59, K:G.149, K:K.216, K:K.216, K:N.246, K:Q.249 Salt bridges: K:D.218 GCP.13: 28 residues within 4Å: Chain M: Q.34, S.35, S.36, G.37, K.38, S.39, S.40, R.53, G.54, T.55, G.56, I.57, V.58, T.59, P.148, G.149, T.215, K.216, D.218, L.219, V.244, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.14 18 PLIP interactions: 18 interactions with chain M Hydrogen bonds: M:S.35, M:S.36, M:G.37, M:K.38, M:K.38, M:S.39, M:S.40, M:S.40, M:G.54, M:G.54, M:V.58, M:T.59, M:G.149, M:K.216, M:K.216, M:N.246, M:Q.249 Salt bridges: M:D.218 GCP.15: 28 residues within 4Å: Chain O: Q.34, S.35, S.36, G.37, K.38, S.39, S.40, R.53, G.54, T.55, G.56, I.57, V.58, T.59, P.148, G.149, T.215, K.216, D.218, L.219, V.244, V.245, N.246, R.247, S.248, Q.249, I.252 Ligands: MG.16 18 PLIP interactions: 18 interactions with chain O Hydrogen bonds: O:S.35, O:S.36, O:G.37, O:K.38, O:K.38, O:S.39, O:S.40, O:S.40, O:G.54, O:G.54, O:V.58, O:T.59, O:G.149, O:K.216, O:K.216, O:N.246, O:Q.249 Salt bridges: O:D.218

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.38, S.39, V.58, T.59, D.146 Ligands: GCP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.39, A:T.59 MG.4: 6 residues within 4Å: Chain C: K.38, S.39, V.58, T.59, D.146 Ligands: GCP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.39, C:T.59 MG.6: 6 residues within 4Å: Chain E: K.38, S.39, V.58, T.59, D.146 Ligands: GCP.5 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.39, E:T.59 MG.8: 6 residues within 4Å: Chain G: K.38, S.39, V.58, T.59, D.146 Ligands: GCP.7 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:S.39, G:T.59 MG.10: 6 residues within 4Å: Chain I: K.38, S.39, V.58, T.59, D.146 Ligands: GCP.9 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:S.39, I:T.59 MG.12: 6 residues within 4Å: Chain K: K.38, S.39, V.58, T.59, D.146 Ligands: GCP.11 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:S.39, K:T.59 MG.14: 6 residues within 4Å: Chain M: K.38, S.39, V.58, T.59, D.146 Ligands: GCP.13 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:S.39, M:T.59 MG.16: 6 residues within 4Å: Chain O: K.38, S.39, V.58, T.59, D.146 Ligands: GCP.15 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:S.39, O:T.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalia, R. et al., Structural basis of mitochondrial receptor binding and constriction by DRP1. Nature (2018)

Release Date

2018-06-20

Peptides

Dynamin-1-like protein: ACEGIKMO
Mitochondrial dynamics protein MID49: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

Dynamin-1-like protein

Mitochondrial dynamics protein MID49