SMTL ID : 7yne.2 (3 other biounits)

Crystal structure of fragmin domain-1 (1-160) in complex with G-form actin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: CA.2 14 PLIP interactions: 14 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:K.215, A:E.216, A:G.304, A:K.338 Water bridges: A:K.20 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: Q.139 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) CA.4: 4 residues within 4Å: Chain A: E.169 Chain B: D.117, G.122, P.124 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.117, B:G.122, B:P.124, H2O.2, H2O.2 CA.5: 4 residues within 4Å: Chain B: G.71, D.72, E.105, V.154 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.71, B:D.72, B:E.105, B:E.105, H2O.5

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

NA.3: 2 residues within 4Å: Chain A: V.32, D.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.58

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

ACT.6: 5 residues within 4Å: Chain B: R.51, V.60, P.61, H.64, Y.69 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.60 Salt bridges: B:R.51, B:H.64

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

PO4.7: 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:I.49, B:W.50, B:V.60 Salt bridges: B:H.65

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
C

B
D

Actin, alpha skeletal muscle

Actin-binding protein fragmin P

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