SMTL ID : 6rla.1

Structure of the dynein-2 complex; motor domains

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: L.1868, V.1869, G.1898, T.1899, G.1900, K.1901, T.1902, E.1903, L.2072, R.2073, K.2076, D.2277, D.2278 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:V.1869, A:V.1869, A:G.1898, A:T.1899, A:G.1900, A:K.1901, A:T.1902, A:T.1902, A:E.1903, A:K.2076, A:D.2278, A:D.2278, A:R.2315 Salt bridges: A:K.1901, A:R.2073, A:R.2073 ADP.4: 13 residues within 4Å: Chain A: L.2466, M.2474, G.2500, C.2501, G.2502, K.2503, G.2504, M.2505, K.2565, I.2647, Y.2651, C.2703, T.2706 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.2500, A:C.2501, A:G.2502, A:K.2503, A:G.2504, A:M.2505, A:T.2706 Salt bridges: A:K.2503, A:K.2503, A:K.2565, A:K.2565 ADP.5: 12 residues within 4Å: Chain A: D.2832, I.2833, L.2834, F.2836, V.2839, G.2864, V.2865, G.2866, R.2867, R.2868, T.2869, R.3547 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.2834, A:G.2864, A:G.2866, A:R.2867, A:R.2868, A:R.2868, A:T.2869, A:T.2869 Salt bridges: A:R.2867 ADP.6: 13 residues within 4Å: Chain B: L.1868, V.1869, G.1898, T.1899, G.1900, K.1901, T.1902, E.1903, L.2072, R.2073, K.2076, D.2277, D.2278 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:V.1869, B:V.1869, B:G.1898, B:T.1899, B:G.1900, B:K.1901, B:T.1902, B:T.1902, B:E.1903, B:K.2076, B:D.2278, B:D.2278, B:R.2315 Salt bridges: B:K.1901, B:R.2073, B:R.2073 ADP.9: 13 residues within 4Å: Chain B: L.2466, M.2474, G.2500, C.2501, G.2502, K.2503, G.2504, M.2505, K.2565, I.2647, Y.2651, C.2703, T.2706 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.2500, B:C.2501, B:G.2502, B:K.2503, B:G.2504, B:M.2505, B:T.2706 Salt bridges: B:K.2503, B:K.2503, B:K.2565, B:K.2565 ADP.10: 12 residues within 4Å: Chain B: D.2832, I.2833, L.2834, F.2836, V.2839, G.2864, V.2865, G.2866, R.2867, R.2868, T.2869, R.3547 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:L.2834, B:G.2864, B:G.2866, B:R.2867, B:R.2868, B:R.2868, B:T.2869, B:T.2869 Salt bridges: B:R.2867

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

ATP.2: 17 residues within 4Å: Chain A: Y.2158, E.2159, Q.2164, P.2186, S.2187, G.2188, A.2189, G.2190, K.2191, S.2192, T.2193, E.2301, S.2330, L.2331, S.2334, R.2626 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.2159, A:Q.2164, A:Q.2164, A:G.2188, A:A.2189, A:G.2190, A:K.2191, A:S.2192, A:S.2192, A:T.2193 Salt bridges: A:K.2191, A:K.2191, A:R.2626 ATP.7: 17 residues within 4Å: Chain B: Y.2158, E.2159, Q.2164, P.2186, S.2187, G.2188, A.2189, G.2190, K.2191, S.2192, T.2193, E.2301, S.2330, L.2331, S.2334, R.2626 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:E.2159, B:Q.2164, B:Q.2164, B:G.2188, B:A.2189, B:G.2190, B:K.2191, B:S.2192, B:S.2192, B:T.2193 Salt bridges: B:K.2191, B:K.2191, B:R.2626

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.2192, E.2301 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2192, A:E.2301 MG.8: 3 residues within 4Å: Chain B: S.2192, E.2301 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.2192, B:E.2301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toropova, K. et al., Structure of the dynein-2 complex and its assembly with intraflagellar transport trains. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-08-28

Peptides

O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein

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