SMTL ID : 7z8m.1

The pointed end complex of dynactin bound to BICDR1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain D: C.30, C.33, C.284, C.287 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.30, D:C.33, D:C.284, D:C.287 ZN.2: 4 residues within 4Å: Chain D: C.51, C.54, C.70, C.73 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.51, D:C.54, D:C.70, D:C.73 ZN.3: 4 residues within 4Å: Chain D: C.76, C.79, C.111, C.114 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.76, D:C.79, D:C.111, D:C.114

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

ATP.4: 22 residues within 4Å: Chain D: L.252, R.255, Q.262 Chain E: G.21, E.22, A.23, F.24, K.26, G.142, Y.143, R.144, G.168, H.172, E.208, K.211, V.212, G.307, G.308, T.309, M.311, N.351 Ligands: MG.5 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:E.22, E:A.23, E:F.24, E:F.24, E:Y.143, E:R.144, E:E.208, E:E.208, E:K.211, E:G.308, E:N.351, D:R.255, D:Q.262 Salt bridges: E:K.26, E:K.26

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

MG.5: 2 residues within 4Å: Chain E: D.140 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain F: Q.142, D.159 Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain I: D.15, Q.142, T.340 Ligands: ADP.10 No protein-ligand interaction detected (PLIP)

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

ADP.6: 15 residues within 4Å: Chain F: G.17, S.18, V.20, K.22, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:S.18, F:V.20, F:D.162, F:D.162, F:K.215, F:K.215, F:K.218, F:G.303, F:L.306 Salt bridges: F:K.22, F:K.22 pi-Stacking: F:F.307 ADP.8: 18 residues within 4Å: Chain G: D.11, G.13, S.14, G.15, M.16, K.18, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.9 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:S.14, G:G.15, G:M.16, G:M.16, G:D.157, G:D.157, G:K.213, G:E.214, G:G.302, G:T.303, G:K.336 Salt bridges: G:K.18, G:K.18 pi-Stacking: G:Y.306 ADP.10: 18 residues within 4Å: Chain I: D.15, G.17, S.18, V.20, K.22, D.159, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 Ligands: MG.11 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:D.15, I:S.18, I:V.20, I:D.162, I:D.162, I:D.162, I:K.218, I:E.219, I:E.219, I:G.303 Salt bridges: I:K.22, I:K.22 pi-Stacking: I:F.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaaban, S. et al., Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Nature (2022)

Release Date

2022-07-27

Peptides

Dynactin subunit 2: A
BICD family-like cargo adapter 1: B
Dynactin 6: C
Dynactin subunit 4: D
Arp11: E
ARP1 actin related protein 1 homolog A: FI
Actin, cytoplasmic 1: G
Dynactin subunit 5: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
X

C
U

D
Y

E
J

F
G

I
I

G
H

H
V

Dynactin subunit 2

BICD family-like cargo adapter 1

Dynactin 6

Dynactin subunit 4

Arp11

ARP1 actin related protein 1 homolog A

Actin, cytoplasmic 1

Dynactin subunit 5

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