SMTL ID : 5o2z.1

Domain swap dimer of the G167R variant of gelsolin second domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: G.39, D.40, N.59, E.62 Ligands: FLC.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.39, A:D.40, A:E.62, A:E.62, H2O.1 CA.7: 5 residues within 4Å: Chain B: G.39, D.40, N.59, E.62 Ligands: FLC.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.39, B:D.40, B:E.62, B:E.62, H2O.1

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 12 residues within 4Å: Chain A: R.20, G.39, D.40, N.57, S.58, N.59, E.62, G.109 Chain B: K.19, R.60, Y.61 Ligands: CA.1 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:Y.61, A:N.59, A:N.59, A:E.62 Water bridges: B:K.19, B:R.20, A:R.20, A:R.20, A:A.108, A:T.110, A:T.110 Salt bridges: B:K.19, B:R.60, A:R.20, A:R.20 FLC.8: 13 residues within 4Å: Chain A: K.19, R.22, Y.61 Chain B: R.20, G.39, D.40, N.57, S.58, N.59, E.62, G.109, T.110 Ligands: CA.7 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Water bridges: A:R.20, A:Y.61, B:R.20, B:R.20 Salt bridges: A:K.19, A:R.22, A:R.22, B:R.20, B:R.20 Hydrogen bonds: B:N.59, B:N.59, B:T.110

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: F.16 Chain B: A.26, V.69 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.26 ACT.4: 6 residues within 4Å: Chain A: V.10, V.11, V.12 Chain B: D.45, G.47, R.78 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.11 Hydrogen bonds: A:V.12 Water bridges: B:G.47, B:R.78 Salt bridges: B:R.78

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: V.86, S.87, T.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.86, A:T.91 NA.6: 3 residues within 4Å: Chain A: G.47, N.48, R.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.47

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain B: V.84, H.85, V.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.85, B:V.86 Water bridges: B:R.83, B:V.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boni, F. et al., Gelsolin pathogenic Gly167Arg mutation promotes domain-swap dimerization of the protein. Hum. Mol. Genet. (2018)

Release Date

2017-11-08

Peptides

Gelsolin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Gelsolin