SMTL ID : 6ljd.1

Crystal structure of fragmin F2-F3 domains (calcium condition)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: G.33, D.34, E.56, D.108 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.56, A:E.56, A:D.108, H2O.1, H2O.5 CA.2: 4 residues within 4Å: Chain A: S.124, N.149, D.150, E.172 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.149, A:D.150, A:E.172, H2O.3, H2O.5 CA.3: 3 residues within 4Å: Chain A: E.62, D.209, D.212 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.62, A:D.209, A:D.209, A:D.212, A:D.212

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: K.15, G.53, L.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.54 Water bridges: A:K.15, A:K.15, A:L.55 Salt bridges: A:K.15

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: E.70, R.71, E.159, F.161, A.196, V.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.71, A:E.159 Water bridges: A:E.70

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: S.107, D.108, L.109 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 6 residues within 4Å: Chain A: R.143, L.146, S.148, W.163, E.200, G.201 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.143, A:G.201 Water bridges: A:R.143, A:S.148, A:W.163, A:E.200 Salt bridges: A:R.143, A:E.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeda, S. et al., Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin. J.Muscle Res.Cell.Motil. (2020)

Release Date

2020-01-01

Peptides

Actin-binding protein fragmin P: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Actin-binding protein fragmin P

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