SMTL ID : 8wdb.1

Cryo-EM structure of the ATP-bound DppABCD complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.1: 20 residues within 4Å: Chain A: F.18, A.24, E.43, S.44, G.45, S.46, G.47, K.48, S.49, T.50, P.60, Q.98, H.212, R.427, R.430, E.431, S.433, G.434, G.435 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.45, A:G.45, A:S.46, A:G.47, A:K.48, A:S.49, A:T.50, A:T.50, A:Q.98, A:R.427, A:R.427, A:R.430, A:S.433, A:G.434, A:G.435 Salt bridges: A:K.48, A:K.48, A:H.212 pi-Stacking: A:F.18, A:F.18 ATP.2: 21 residues within 4Å: Chain A: R.149, H.152, Q.153, S.155, G.156, G.157, M.158, A.183, Y.291, A.306, S.326, G.327, S.328, G.329, K.330, S.331, T.332, Q.376, Q.457, H.490 Ligands: MG.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.149, A:R.149, A:H.152, A:S.155, A:G.156, A:G.157, A:A.183, A:G.327, A:S.328, A:G.329, A:K.330, A:S.331, A:T.332, A:T.332, A:Q.376, A:Q.457 Salt bridges: A:K.330, A:K.330, A:H.490 pi-Stacking: A:Y.291, A:Y.291

2 x MG: MAGNESIUM ION

MG.3: 3 residues within 4Å: Chain A: S.49, Q.98 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.49 MG.4: 3 residues within 4Å: Chain A: S.331, Q.376 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2024-09-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

C
C

D
A

Membrane

We predict this structure to be a membrane protein.
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Probable dipeptide-transport ATP-binding protein ABC transporter DppD

Probable dipeptide-transport integral membrane protein ABC transporter DppB

Probable dipeptide-transport integral membrane protein ABC transporter DppC

Probable periplasmic dipeptide-binding lipoprotein DppA

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