SMTL ID : 9c5a.1

AP-3 Arf1 dimeric interface, focused refinement

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

GTP.2: 20 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:A.26, C:A.27, C:G.28, C:K.29, C:T.30, C:T.30, C:T.31, C:T.31, C:T.44, C:T.47, C:G.69, C:N.125, C:K.126, C:K.126, C:A.159, C:T.160 Salt bridges: C:K.29, C:K.29, C:D.128 GTP.4: 20 residues within 4Å: Chain G: 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.3 19 PLIP interactions: 19 interactions with chain G Hydrogen bonds: G:A.26, G:A.27, G:G.28, G:K.29, G:T.30, G:T.30, G:T.31, G:T.31, G:T.44, G:T.47, G:G.69, G:N.125, G:K.126, G:K.126, G:A.159, G:T.160 Salt bridges: G:K.29, G:K.29, G: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

AP-3 complex subunit beta-1: AE
AP-3 complex subunit mu-1: BF
ADP-ribosylation factor 1: CG
Lysosome-associated membrane glycoprotein 1: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E
b

B
M

F
m

C
C

G
c

D
Y

H
y

AP-3 complex subunit beta-1

AP-3 complex subunit mu-1

ADP-ribosylation factor 1

Lysosome-associated membrane glycoprotein 1

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