SMTL ID : 8wda.1

Cryo-EM structure of the substrate-bound DppABCD complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ALA- VAL- ALA- ALA: tetrapeptide

ALA-VAL-ALA-ALA.1: 13 residues within 4Å: Chain A: N.28, D.29, S.30, N.31, N.366, A.369, H.371, F.398, R.415, G.417, W.418, R.419, D.421 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.29, A:W.418 Hydrogen bonds: A:N.28, A:S.30, A:S.30, A:S.30, A:N.366, A:R.415, A:R.419, A:D.421 Salt bridges: A:H.371, A:R.415

1 x PLM: PALMITIC ACID

PLM.2: 3 residues within 4Å: Chain A: C.1 Chain B: S.171 Ligands: 9XX.3 No protein-ligand interaction detected (PLIP)

1 x 9XX: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

9XX.3: 6 residues within 4Å: Chain A: C.1 Chain B: R.100, L.103, A.107, V.172 Ligands: PLM.2 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.100, B:L.103, B:A.107, B:V.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, T. et al., Cryo-EM structure of the substrate-bound DppABCD complex. To Be Published

Release Date

2024-09-18

Peptides

Probable periplasmic dipeptide-binding lipoprotein DppA: A
Probable dipeptide-transport integral membrane protein ABC transporter DppB: B
Probable dipeptide-transport integral membrane protein ABC transporter DppC: C
Probable dipeptide-transport ATP-binding protein ABC transporter DppD: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Probable periplasmic dipeptide-binding lipoprotein DppA

Probable dipeptide-transport integral membrane protein ABC transporter DppB

Probable dipeptide-transport integral membrane protein ABC transporter DppC

Probable dipeptide-transport ATP-binding protein ABC transporter DppD

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