SMTL ID : 7w51.1

Crystal structure of fragmin domain-1 in complex with actin (ADP-form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:L.18, A:D.159, A:D.159, A:G.160, A:K.215, A:G.304, A:K.338 Water bridges: A:D.13, A:K.20, A:K.20, A:G.158, A:E.216, A:E.216, A:E.216, A:E.216, A:M.307, A:K.338 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308

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

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

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

EDO.3: 6 residues within 4Å: Chain A: Y.135, A.137, I.138, V.141, F.354, F.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.135, A:I.138 EDO.4: 9 residues within 4Å: Chain A: N.14, I.73, G.76, I.78, T.108, E.109, N.117, M.121, Q.139 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.78, A:T.108, A:N.117, A:N.117, A:Q.139 Water bridges: A:T.108, A:N.113 EDO.7: 4 residues within 4Å: Chain B: Y.80, D.92, R.137 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.92, B:R.137 Water bridges: B:Y.80 EDO.8: 5 residues within 4Å: Chain B: S.78, Y.80, D.92, L.141 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.78, B:S.78, B:D.92 EDO.9: 6 residues within 4Å: Chain B: E.48, I.49, W.50, P.59, V.60, H.65 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.48, B:E.48, B:I.49, B:H.65 Water bridges: B:K.62

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: E.169 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.169, H2O.29, H2O.29 CA.6: 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.27, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanematsu, Y. et al., Structures and mechanisms of actin ATP hydrolysis. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-10-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Actin, alpha skeletal muscle

Actin-binding protein fragmin P

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