SMTL ID : 6znm.1

The pointed end complex of dynactin bound to BICDR1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-1-1-2-1-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:D.15, A:S.18, 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:Q.142, C:Q.142, C:D.162, C:D.162, C:K.218, C:G.303, C:L.337 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 I: R.255, Q.262 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain I 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, I:R.255, I: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 I: C.30, C.33, R.37, C.287 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.33, I:C.287 ZN.6: 4 residues within 4Å: Chain I: C.51, C.54, C.70, C.73 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.51, I:C.70 ZN.7: 4 residues within 4Å: Chain I: C.76, C.79, C.111, C.114 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.76, I: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
Dynactin 6: F
Dynactin subunit 5: G
BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR1: HJ
Dynactin subunit 4: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
I

B
H

D
J

E
M

F
U

G
V

H
X

J
x

I
Y

ARP1 actin related protein 1 homolog A

Actin, cytoplasmic 1

Arp11

Dynactin subunit 2

Dynactin 6

Dynactin subunit 5

BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR1

Dynactin subunit 4

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