SMTL ID : 6sc2.1

Structure of the dynein-2 complex; IFT-train bound model

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-2-2-6-mer

Ligands

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

ADP.1: 9 residues within 4Å: Chain A: L.1868, V.1869, G.1898, T.1899, G.1900, K.1901, T.1902, E.1903, D.2278 8 PLIP interactions: 8 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:E.1903 ADP.4: 7 residues within 4Å: Chain A: G.2500, C.2501, G.2502, K.2503, G.2504, M.2505, T.2706 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.2500, A:C.2501, A:G.2502, A:K.2503, A:G.2504, A:M.2505 ADP.5: 9 residues within 4Å: Chain A: D.2832, I.2833, L.2834, G.2864, V.2865, G.2866, R.2867, R.2868, T.2869 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.2834, A:G.2864, A:G.2866, A:R.2867, A:R.2868, A:T.2869 ADP.6: 9 residues within 4Å: Chain B: L.1868, V.1869, G.1898, T.1899, G.1900, K.1901, T.1902, E.1903, D.2278 8 PLIP interactions: 8 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:E.1903 ADP.9: 7 residues within 4Å: Chain B: G.2500, C.2501, G.2502, K.2503, G.2504, M.2505, T.2706 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.2500, B:C.2501, B:G.2502, B:K.2503, B:G.2504, B:M.2505 ADP.10: 9 residues within 4Å: Chain B: D.2832, I.2833, L.2834, G.2864, V.2865, G.2866, R.2867, R.2868, T.2869 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.2834, B:G.2864, B:G.2866, B:R.2867, B:R.2868, B:T.2869

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

ATP.2: 12 residues within 4Å: Chain A: Y.2158, E.2159, P.2186, S.2187, G.2188, A.2189, G.2190, K.2191, S.2192, T.2193, S.2330 Ligands: MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.2159, A:E.2159, A:G.2188, A:A.2189, A:G.2190, A:K.2191, A:S.2192, A:T.2193 ATP.7: 12 residues within 4Å: Chain B: Y.2158, E.2159, P.2186, S.2187, G.2188, A.2189, G.2190, K.2191, S.2192, T.2193, S.2330 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.2159, B:E.2159, B:G.2188, B:A.2189, B:G.2190, B:K.2191, B:S.2192, B:T.2193

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.2192 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: S.2192 Ligands: ATP.7 No protein-ligand interaction detected (PLIP)

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

2019-09-04

Peptides

O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein: A
O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein: B
WD repeat-containing protein 60: C
WD repeat-containing protein 34: D
Cytoplasmic dynein 2 light intermediate chain 1: EF
Dynein light chain roadblock-type 1: GH
Dynein light chain 1, cytoplasmic: IJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein

O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein

WD repeat-containing protein 60

WD repeat-containing protein 34

Cytoplasmic dynein 2 light intermediate chain 1

Dynein light chain roadblock-type 1

Dynein light chain 1, cytoplasmic

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