SMTL ID : 6nbw.1

Ternary Complex of Beta/Gamma-Actin with Profilin and AnCoA-NAA80

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: G.12, K.17, Q.136 Ligands: ATP.2 No protein-ligand interaction detected (PLIP)

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

ATP.2: 24 residues within 4Å: Chain A: G.12, S.13, G.14, M.15, K.17, G.73, G.155, D.156, G.157, V.158, G.181, R.182, T.185, R.209, K.212, E.213, G.300, G.301, T.302, M.304, Y.305, K.335 Ligands: CA.1, LAB.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:S.13, A:S.13, A:G.14, A:M.15, A:M.15, A:G.155, A:D.156, A:G.157, A:V.158, A:K.212, A:E.213, A:G.301, A:K.335 Water bridges: A:K.17, A:K.17, A:K.17, A:Q.136, A:Q.136, A:E.213, A:E.213, A:Y.305, A:K.335 Salt bridges: A:K.17, A:K.17 pi-Stacking: A:Y.305

1 x LAB: LATRUNCULIN B(Non-covalent)

LAB.3: 19 residues within 4Å: Chain A: G.14, M.15, P.31, S.32, I.33, Q.58, R.61, L.66, Y.68, D.156, G.181, R.182, T.185, R.205, E.206, R.209, K.212, E.213 Ligands: ATP.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.31, A:I.33, A:Q.58, A:L.66, A:E.206 Hydrogen bonds: A:Y.68, A:D.156, A:T.185, A:R.209, A:K.212 Salt bridges: A:R.209

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: S.13, I.70, E.71, H.72, D.156, G.157, R.182, D.183 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.182, A:D.183 Water bridges: A:E.71, A:R.182, A:R.182 GOL.5: 7 residues within 4Å: Chain A: Y.197, S.198, F.199, E.204, L.241, Q.245, I.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.198, A:S.198, A:E.204 Water bridges: A:S.198

1 x SOP: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

SOP.6: 25 residues within 4Å: Chain B: H.3, Q.31, W.32, V.87, E.88, T.89, V.90, V.91, V.92, R.97, G.98, R.99, G.100, F.101, G.102, R.103, L.123, T.124, T.125, Q.128, H.130, F.131, Y.132, H.134, L.135 27 PLIP interactions: 26 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.31, B:W.32, B:V.90 Hydrogen bonds: B:H.3, B:H.3, B:T.89, B:V.90, B:V.90, B:V.92, B:G.98, B:G.100, B:G.100, B:F.101, B:G.102, B:R.103 Water bridges: B:R.99, B:R.99, B:R.103, B:Q.128, B:F.131, B:F.131, A:D.1 Salt bridges: B:H.3, B:H.3, B:R.103, B:H.134 pi-Stacking: B:F.131

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 7 residues within 4Å: Chain B: F.50, R.77, P.82, Q.83, R.116, G.117, F.118 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.117 Salt bridges: B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rebowski, G. et al., Mechanism of actin N-terminal acetylation. Sci Adv (2020)

Release Date

2020-01-29

Peptides

Actin, cytoplasmic 1: A
N-alpha-acetyltransferase 80: B
Profilin-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
N

C
P

Actin, cytoplasmic 1

N-alpha-acetyltransferase 80

Profilin-1

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