SMTL ID : 5owo.1

Human cytoplasmic Dynein N-Terminus dimerization domain at 1.8 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-tetramer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: A.51, E.97, F.98, I.99 Chain C: F.98 Ligands: MG.5, GOL.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.99, A:I.99 GOL.2: 6 residues within 4Å: Chain A: E.147, H.150, S.151, S.154, N.155 Chain D: H.75 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:E.147, A:S.154, A:N.155, D:H.75, D:H.75 GOL.3: 6 residues within 4Å: Chain A: A.127, D.128, K.129, P.130 Chain D: D.44 Ligands: MG.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.128, D:D.44 Water bridges: A:V.131 GOL.13: 4 residues within 4Å: Chain B: A.51, E.97, F.98, I.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.97, B:I.99 Water bridges: B:A.51, B:I.99 GOL.14: 6 residues within 4Å: Chain B: H.75, T.122, P.123 Chain C: E.147 Ligands: MG.16, GOL.26 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.122, C:E.147, C:E.147 Water bridges: B:R.136 GOL.15: 3 residues within 4Å: Chain B: E.147, H.150, L.194 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.147 GOL.25: 7 residues within 4Å: Chain A: F.98 Chain C: A.51, E.97, F.98, I.99 Ligands: GOL.1, MG.27 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.97, C:I.99, C:I.99 GOL.26: 7 residues within 4Å: Chain B: H.75 Chain C: E.147, H.150, S.151, S.154, N.155 Ligands: GOL.14 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.147, C:H.150, C:S.154, C:N.155, C:N.155, B:H.75 Water bridges: B:R.136 GOL.34: 5 residues within 4Å: Chain D: A.51, E.97, F.98, I.99 Ligands: MG.35 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.99 Water bridges: D:I.99

26 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 4 residues within 4Å: Chain A: L.78, N.104, D.106, H.108 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.106, H2O.3, H2O.3 MG.5: 5 residues within 4Å: Chain A: P.49, A.50, A.51 Chain C: F.98 Ligands: GOL.1 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: T.83, K.112, N.114, E.142 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: GOL.3 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: F.152, V.157 Chain D: F.152, V.157 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain A: E.58, K.59 Chain C: E.80 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain A: S.132, L.135, R.136, V.137 Chain D: T.139 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.135, H2O.3 MG.11: 3 residues within 4Å: Chain A: H.195, Q.198, N.199 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain B: P.72, H.75, P.123 Ligands: GOL.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.72 MG.17: 3 residues within 4Å: Chain B: S.154, A.158, E.190 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.154, B:E.190 MG.18: 4 residues within 4Å: Chain B: K.162, E.183, I.186, A.187 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.183, H2O.4, H2O.5 MG.19: 2 residues within 4Å: Chain B: K.32, R.35 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain B: H.195, Q.198, N.199 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain B: Y.164 Chain C: S.144, P.145, I.200 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:Y.164, C:S.144 MG.22: 4 residues within 4Å: Chain B: L.78, N.104, D.106, H.108 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.106, H2O.5 MG.23: 1 residues within 4Å: Chain B: E.188 No protein-ligand interaction detected (PLIP) MG.27: 5 residues within 4Å: Chain A: F.98 Chain C: P.49, A.50, A.51 Ligands: GOL.25 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain C: T.83, K.112, N.114, E.142 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain C: P.72, H.75, P.123 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:P.72 MG.30: 5 residues within 4Å: Chain B: F.152, V.157 Chain C: L.138, F.152, V.157 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain C: A.25, D.26, V.29, A.127 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain C: Q.73, V.74, H.75, T.76 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain C: T.122, P.123, V.124 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:V.124 MG.35: 4 residues within 4Å: Chain D: P.49, A.50, A.51 Ligands: GOL.34 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain D: G.110, V.111, K.112, S.113 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.113 MG.37: 3 residues within 4Å: Chain D: P.72, H.75, P.123 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:P.72

2 x CA: CALCIUM ION(Non-covalent)

CA.12: 4 residues within 4Å: Chain A: E.58, N.102 Chain C: E.58, N.102 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:E.58, A:E.58, A:E.58, H2O.1, H2O.6 CA.38: 3 residues within 4Å: Chain D: E.58, N.102 Ligands: K.39 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.58, D:E.58, H2O.9

1 x NA: SODIUM ION(Non-functional Binders)

NA.24: 2 residues within 4Å: Chain B: E.58, N.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.58

1 x K: POTASSIUM ION(Non-covalent)

K.39: 4 residues within 4Å: Chain D: E.58, S.60, N.102 Ligands: CA.38 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Urnavicius, L. et al., Cryo-EM shows how dynactin recruits two dyneins for faster movement. Nature (2018)

Release Date

2018-07-11

Peptides

Cytoplasmic dynein 1 heavy chain 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cytoplasmic dynein 1 heavy chain 1