SMTL ID : 7w50.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 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.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: PO4.2, MG.3 21 PLIP interactions: 21 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:E.216, 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

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

PO4.2: 9 residues within 4Å: Chain A: S.16, G.76, Q.139, G.158, D.159, G.160, V.161 Ligands: ADP.1, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.16, A:S.16, A:G.158, A:G.160, A:V.161 Water bridges: A:Q.139, A:Q.139, A:Q.139, A:D.156, A:D.156, A:S.157, A:V.161 PO4.4: 1 residues within 4Å: Chain A: R.97 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.97, A:R.97, A:R.97 Salt bridges: A:R.97 PO4.5: 2 residues within 4Å: Chain A: R.41, H.42 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.41, A:H.42 Salt bridges: A:R.41, A:H.42

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)

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

EDO.6: 6 residues within 4Å: Chain A: Y.135, A.137, I.138, V.141, F.354, F.377 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.135, A:I.138 Water bridges: A:F.377, A:F.377, B:K.28 EDO.9: 4 residues within 4Å: Chain B: Y.80, D.92, R.137 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.92, B:R.137 EDO.10: 5 residues within 4Å: Chain B: S.78, Y.80, D.92, L.141 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.78, B:S.78, B:D.92

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.12, H2O.29 CA.8: 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.26, 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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