SMTL ID : 6xjo.1 (2 other biounits)

Human atlastin-3 (residues 1-334) bound to GDP-Mg2+ exhibits an ordered amino terminus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 19 residues within 4Å: Chain A: A.68, F.69, R.70, K.71, G.72, K.73, S.74, F.75, R.109, Q.144, R.213, D.214, H.267, P.268, V.272, A.273, S.275, P.276 Ligands: MG.2 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.70, A:K.71, A:G.72, A:K.73, A:S.74, A:S.74, A:F.75, A:Q.144, A:Q.144, A:R.213, A:H.267 Water bridges: A:S.275, A:P.276, B:S.216, B:S.216 Salt bridges: A:K.73, A:R.109, A:R.109, A:D.214 pi-Cation interactions: A:H.267 GDP.3: 19 residues within 4Å: Chain B: A.68, F.69, R.70, K.71, G.72, K.73, S.74, F.75, R.109, Q.144, R.213, D.214, H.267, P.268, V.272, A.273, S.275, P.276 Ligands: MG.4 24 PLIP interactions: 20 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.70, B:K.71, B:G.72, B:K.73, B:S.74, B:S.74, B:F.75, B:Q.144, B:Q.144, B:R.213, B:H.267 Water bridges: B:R.109, B:R.109, B:D.214, B:P.276, A:S.216, A:Y.219, A:Y.219, A:Y.219 Salt bridges: B:K.73, B:R.109, B:R.109, B:D.214 pi-Cation interactions: B:H.267

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.73, S.74, R.109, D.142, Q.144 Ligands: GDP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.142 MG.4: 5 residues within 4Å: Chain B: K.73, R.109, D.142, Q.144 Ligands: GDP.3 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.142, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kelly, C.M. et al., The hypervariable region of atlastin-1 is a site for intrinsic and extrinsic regulation. J.Cell Biol. (2021)

Release Date

2021-06-30

Peptides

Atlastin-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Atlastin-3

Related Entries With Identical Sequence