SMTL ID : 2a5x.1

Crystal Structure of a Cross-linked Actin Dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

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

CA.1: 1 residues within 4Å: Ligands: ANP.3 No protein-ligand interaction detected (PLIP) CA.2: 2 residues within 4Å: Chain A: Q.263, S.265 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.265, H2O.1, H2O.1, H2O.1 CA.8: 1 residues within 4Å: Ligands: ANP.10 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain B: Q.263, S.265 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.265, H2O.3, H2O.3, H2O.3

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 22 residues within 4Å: Chain A: G.13, S.14, G.15, L.16, K.18, G.74, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.1, LAR.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.14, A:G.15, A:L.16, A:L.16, A:K.18, A:G.156, A:D.157, A:D.157, A:D.157, A:G.158, A:V.159, A:V.159, A:K.213, A:E.214, A:G.302 Water bridges: A:Y.306 Salt bridges: A:K.18 pi-Stacking: A:Y.306 ANP.10: 22 residues within 4Å: Chain B: G.13, S.14, G.15, L.16, K.18, G.74, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: CA.8, LAR.11 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.14, B:G.15, B:L.16, B:L.16, B:K.18, B:G.156, B:D.157, B:D.157, B:G.158, B:V.159, B:V.159, B:K.213, B:E.214, B:E.214, B:G.302, B:T.303 Salt bridges: B:K.18 pi-Stacking: B:Y.306

2 x LAR: LATRUNCULIN A(Non-covalent)

LAR.4: 14 residues within 4Å: Chain A: G.15, L.16, P.32, I.34, Y.69, D.157, G.182, R.183, T.186, R.206, E.207, R.210, K.213 Ligands: ANP.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.34, A:I.34, A:E.207 Hydrogen bonds: A:D.157, A:E.207, A:K.213 Salt bridges: A:R.210 LAR.11: 14 residues within 4Å: Chain B: G.15, L.16, P.32, I.34, Y.69, D.157, G.182, R.183, T.186, R.206, E.207, R.210, K.213 Ligands: ANP.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.34, B:I.34, B:E.207 Hydrogen bonds: B:Y.69, B:D.157, B:T.186, B:E.207, B:K.213 Salt bridges: B:R.210

2 x NSB: N,N,N-TRIMETHYL-3-SULFOPROPAN-1-AMINIUM(Non-covalent)

NSB.5: 5 residues within 4Å: Chain A: Y.218, V.219, K.238, R.254, G.308 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.238, A:R.254 NSB.12: 5 residues within 4Å: Chain B: Y.218, V.219, K.238, R.254, G.308 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.238, B:R.254

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 4 residues within 4Å: Chain A: F.31, P.32, I.34, H.88 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.31 Hydrogen bonds: A:P.32 MPD.7: 7 residues within 4Å: Chain A: Y.133, A.135, I.136, V.139, Y.143, G.168, Y.169 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.135, A:V.139, A:Y.169 Hydrogen bonds: A:I.136, A:Y.143 MPD.13: 4 residues within 4Å: Chain B: F.31, P.32, I.34, H.88 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.31 Hydrogen bonds: B:P.32 MPD.14: 7 residues within 4Å: Chain B: Y.133, A.135, I.136, V.139, Y.143, G.168, Y.169 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.135, B:V.139, B:Y.169 Hydrogen bonds: B:I.136, B:Y.143, B:Y.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kudryashov, D.S. et al., The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin. Proc.Natl.Acad.Sci.Usa (2005)

Release Date

2005-08-23

Peptides

Actin, alpha skeletal muscle: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Actin, alpha skeletal muscle

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