SMTL ID : 6zo4.1

The pointed end complex of dynactin bound to BICD2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 18 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:D.15, C:S.18, C:Q.142, C:Q.142, C:D.162, C:K.215, C:K.218, C:E.219, C:G.303 Salt bridges: C:K.22, C:K.22 pi-Stacking: C:F.307 ADP.3: 16 residues within 4Å: Chain E: 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 E Hydrogen bonds: E:D.15, E:Q.142, E:D.162, E:D.162, E:K.218, E:G.303, E:L.337 Salt bridges: E:K.22, E:K.22 ADP.4: 17 residues within 4Å: Chain F: 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 J: R.255, Q.262 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain J Hydrogen bonds: F:E.22, F:A.23, F:Y.143, F:E.208, F:E.208, F:K.211, F:G.308, F:N.351, J:R.255, J:Q.262 Salt bridges: F:K.26, F:K.26

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

ATP.2: 20 residues within 4Å: Chain D: 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 D Hydrogen bonds: D:G.15, D:M.16, D:Q.137, D:Q.137, D:D.154, D:D.157, D:D.157, D:K.213, D:G.302, D:M.305, D:K.336, D:K.336 Salt bridges: D:K.18, D:K.18, D:K.18, D:K.336

3 x ZN: ZINC ION(Non-covalent)

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

BICD2: AB
ARP1 actin related protein 1 homolog A: CE
Actin, cytoplasmic 1: D
Arp11: F
Dynactin subunit 2: G
Dynactin 6: H
Dynactin subunit 5: I
Dynactin subunit 4: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
5

B
6

C
G

E
I

D
H

F
J

G
M

H
U

I
V

J
Y

BICD2

ARP1 actin related protein 1 homolog A

Actin, cytoplasmic 1

Arp11

Dynactin subunit 2

Dynactin 6

Dynactin subunit 5

Dynactin subunit 4

Related Entries With Identical Sequence