SMTL ID : 8gt3.1

Crystal structure of human cardiac alpha actin P109A mutant (ADP-Pi state) in complex with fragmin F1 domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: G.29, S.30, G.31, L.32, K.34, G.172, D.173, G.174, G.198, R.226, K.229, E.230, G.317, G.318, T.319, M.321, Y.322, K.352 Ligands: PO4.2, MG.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.30, A:G.31, A:L.32, A:L.32, A:D.173, A:D.173, A:D.173, A:G.174, A:K.229, A:E.230, A:G.318, A:T.319 Water bridges: A:K.34, A:T.202, A:E.230, A:E.230, A:E.230, A:E.230, A:E.230, A:M.321, A:Y.322, A:K.352 Salt bridges: A:K.34, A:K.34 pi-Stacking: A:Y.322

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 10 residues within 4Å: Chain A: S.30, G.90, A.124, Q.153, G.172, D.173, G.174, V.175 Ligands: ADP.1, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.30, A:S.30, A:S.30, A:G.172, A:G.174, A:V.175 Water bridges: A:Q.153, A:Q.153, A:Q.153, A:D.170, A:D.170, A:V.175 PO4.4: 1 residues within 4Å: Chain A: R.111 6 PLIP interactions: 6 interactions with chain A Water bridges: A:Y.107, A:R.111, A:R.111, A:R.111, A:R.111 Salt bridges: A:R.111 PO4.5: 2 residues within 4Å: Chain A: R.55, H.56 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.55, A:R.55 Salt bridges: A:R.55, A:H.56

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 2 residues within 4Å: Ligands: ADP.1, PO4.2 No protein-ligand interaction detected (PLIP)

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 7 residues within 4Å: Chain A: Y.149, A.151, I.152, V.155, F.368, F.391 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.152 Water bridges: A:F.391 EDO.7: 9 residues within 4Å: Chain A: V.155, G.184, Y.185, A.186, F.391 Chain B: L.19, E.24, K.28 Ligands: EDO.6 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.186, B:E.24, B:K.28 Water bridges: A:G.184, A:F.391, B:G.20, B:K.28 EDO.10: 4 residues within 4Å: Chain B: Y.80, D.92, R.137 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.92, B:R.137 Water bridges: B:Y.127 EDO.11: 5 residues within 4Å: Chain B: S.78, Y.80, D.92, L.141 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.78, B:S.78

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: E.183 Chain B: D.117, G.122, P.124 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.117, B:P.124, A:E.183, H2O.26, H2O.26 CA.9: 4 residues within 4Å: Chain B: G.71, D.72, E.105, V.154 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.72, B:E.105, B:V.154, H2O.23, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iwasa, M. et al., Mutagenic analysis of actin reveals the mechanism of His161 flipping that triggers ATP hydrolysis. Front Cell Dev Biol (2023)

Release Date

2023-03-08

Peptides

Actin, alpha cardiac muscle 1: A
Actin-binding protein fragmin P: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Actin, alpha cardiac muscle 1

Actin-binding protein fragmin P

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