SMTL ID : 6jsj.1

Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-trimer

Ligands

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

GDP.1: 16 residues within 4Å: Chain A: S.35, Q.36, S.37, S.38, G.39, K.40, S.41, S.42, K.55, T.202, K.203, D.205, L.206, I.231, T.232, K.233 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.37, A:G.39, A:K.40, A:S.41, A:S.41, A:S.41, A:S.42, A:K.203, A:K.203, A:T.232, A:K.233, A:K.233 Salt bridges: A:K.55, A:K.55, A:D.205 GDP.11: 15 residues within 4Å: Chain B: S.35, Q.36, S.37, S.38, G.39, K.40, S.41, S.42, K.55, K.203, D.205, L.206, I.231, T.232, K.233 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.37, B:S.38, B:G.39, B:K.40, B:S.41, B:S.41, B:S.42, B:K.203, B:K.203, B:T.232, B:T.232 Salt bridges: B:K.40, B:D.205 GDP.22: 13 residues within 4Å: Chain C: S.35, S.37, S.38, G.39, K.40, S.41, S.42, K.55, K.203, D.205, I.231, T.232, K.233 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.35, C:S.37, C:G.39, C:K.40, C:S.41, C:S.41, C:S.41, C:S.42, C:S.42, C:K.203, C:T.232 Salt bridges: C:K.40, C:D.205 pi-Cation interactions: C:K.203

25 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: T.395, R.396 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: R.438, M.442 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: L.338, E.342, R.663 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: S.84, M.85, Q.119 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: Q.299, K.308 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: S.352, Y.353, N.356 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: M.442, N.446 Chain B: I.278, H.281 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: V.537 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: M.589 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: V.392, T.395 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain B: R.438, L.439 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain B: E.342, R.663 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain B: R.63, S.84, M.85, Q.119 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain B: N.16, V.18, H.24 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain B: S.35, S.38, S.172, A.173 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain B: N.480, S.481 Chain C: N.76 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain B: M.442, N.446 Chain C: H.281 Ligand excluded by PLIP IOD.20: 6 residues within 4Å: Chain B: T.61, R.63, P.64, I.65, D.134, P.136 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain B: K.220 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain C: R.396 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain C: R.438 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain C: L.338, R.663 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain C: S.84, Q.119 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain C: R.346, Y.353, N.356 Ligand excluded by PLIP IOD.28: 2 residues within 4Å: Chain C: V.537, L.566 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L. et al., Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-02-19

Peptides

Dynamin-like GTPase MGM1, mitochondrial: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Dynamin-like GTPase MGM1, mitochondrial