SMTL ID : 6znn.1

The pointed end complex of dynactin bound to Hook3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: D.15, G.17, S.18, V.20, K.22, Q.142, D.159, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, F.307, L.337 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.18, A:Q.142, A:Q.142, A:Q.142, A:D.162, A:K.215, A:K.218, A:E.219, A:G.303 Salt bridges: A:K.22, A:K.22 pi-Stacking: A:F.307 ADP.3: 16 residues within 4Å: Chain C: D.15, G.17, V.20, K.22, Q.142, D.159, G.161, D.162, K.215, K.218, E.219, G.302, G.303, S.304, L.306, L.337 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:V.20, C:Q.142, C:Q.142, C:D.162, C:D.162, C:K.218, C:G.303 Salt bridges: C:K.22, C:K.22 ADP.4: 17 residues within 4Å: Chain D: G.21, E.22, A.23, F.24, K.26, G.142, Y.143, H.172, E.208, K.211, V.212, G.308, T.309, M.311, N.351 Chain K: R.255, Q.262 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain K Hydrogen bonds: D:E.22, D:A.23, D:Y.143, D:E.208, D:E.208, D:K.211, D:G.308, D:N.351, K:R.255, K:Q.262 Salt bridges: D:K.26, D:K.26

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

ATP.2: 20 residues within 4Å: Chain B: D.11, G.13, S.14, G.15, M.16, K.18, Q.137, D.154, G.156, D.157, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336, V.339 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.15, B:M.16, B:Q.137, B:Q.137, B:D.154, B:D.157, B:D.157, B:K.213, B:G.302, B:M.305, B:K.336, B:K.336 Salt bridges: B:K.18, B:K.18, B:K.18, B:K.336

3 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain K: C.30, C.33, R.37, C.287 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:C.33, K:C.287 ZN.6: 4 residues within 4Å: Chain K: C.51, C.54, C.70, C.73 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:C.51, K:C.70 ZN.7: 4 residues within 4Å: Chain K: C.76, C.79, C.111, C.114 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:C.76, K:C.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lau, C.K. et al., Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end. Embo J. (2021)

Release Date

2020-07-29

Peptides

ARP1 actin related protein 1 homolog A: AC
Actin, cytoplasmic 1: B
Arp11: D
Dynactin subunit 2: E
putative Hook3 coiled coil: FG
Dynactin 6: H
Dynactin subunit 5: I
Hook3: J
Dynactin subunit 4: K
Hook3: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
I

B
H

D
J

E
M

F
S

G
T

H
U

I
V

J
X

K
Y

L
x

ARP1 actin related protein 1 homolog A

Actin, cytoplasmic 1

Arp11

Dynactin subunit 2

putative Hook3 coiled coil

Dynactin 6

Dynactin subunit 5

Hook3

Dynactin subunit 4

Hook3

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