SMTL ID : 9c5b.1

AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.30, T.47 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.30, A:T.47 MG.3: 4 residues within 4Å: Chain B: T.30, T.47, D.66 Ligands: GTP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.30, B:T.47

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 20 residues within 4Å: Chain A: L.24, D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.44, T.47, G.68, G.69, N.125, K.126, D.128, L.129, C.158, A.159, T.160 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:A.26, A:A.27, A:G.28, A:K.29, A:T.30, A:T.31, A:T.31, A:T.44, A:T.47, A:G.69, A:L.70, A:N.125, A:K.126, A:K.126, A:A.159, A:T.160 Salt bridges: A:K.29, A:K.29, A:D.128 GTP.4: 19 residues within 4Å: Chain B: L.24, D.25, A.26, A.27, G.28, K.29, T.30, T.31, T.47, G.68, G.69, N.125, K.126, D.128, L.129, C.158, A.159, T.160 Ligands: MG.3 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.26, B:A.27, B:G.28, B:K.29, B:T.30, B:T.30, B:T.31, B:T.31, B:T.47, B:G.69, B:N.125, B:K.126, B:K.126, B:A.159, B:T.160, B:T.160 Salt bridges: B:K.29, B:D.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Begley, M. et al., A structure-based mechanism for initiation of AP-3 coated vesicle formation. To Be Published

Release Date

2024-12-18

Peptides

ADP-ribosylation factor 1: AB
AP-3 complex subunit delta-1: C
AP-3 complex subunit mu-1: D
AP-3 complex subunit sigma-1: E
Lysosome-associated membrane glycoprotein 1: F
AP-3 complex subunit beta-1: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
M

E
S

F
Y

G
B

ADP-ribosylation factor 1

AP-3 complex subunit delta-1

AP-3 complex subunit mu-1

AP-3 complex subunit sigma-1

Lysosome-associated membrane glycoprotein 1

AP-3 complex subunit beta-1

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