SMTL ID : 7w52.2 (3 other biounits)

Crystal structure of fragmin domain-1 (15-160) in complex with actin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.76, G.158, D.159, G.160, V.161, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: CA.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:G.158, A:D.159, A:D.159, A:D.159, A:G.160, A:V.161, A:V.161, A:K.215, A:E.216, A:G.304, A:K.338 Water bridges: A:K.20, A:K.20, A:D.156, A:D.156, A:D.156, A:D.156, A:Y.308, A:K.338 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308

3 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) CA.5: 4 residues within 4Å: Chain A: E.169 Chain B: D.103, G.108, P.110 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.103, B:G.108, B:P.110, H2O.8, H2O.15 CA.6: 4 residues within 4Å: Chain B: G.57, D.58, E.91, V.140 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.57, B:D.58, B:V.140, H2O.14, H2O.14

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

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

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

EDO.4: 5 residues within 4Å: Chain A: Y.135, A.137, I.138, V.141, F.377 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.135, A:I.138 Water bridges: B:K.14, B:K.14, B:K.14, B:Y.97

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

ACT.7: 5 residues within 4Å: Chain B: R.37, V.46, P.47, H.50, Y.55 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.46 Salt bridges: B:R.37, B:H.50

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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