SMTL ID : 8z1y.1

Cryo-EM structure of Escherichia coli DppABCDF in the pre-catalytic state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 20 residues within 4Å: Chain C: F.13, F.20, A.22, S.42, G.43, S.44, G.45, K.46, S.47, V.48, Q.96, Q.179, H.212 Chain D: R.157, M.161, S.163, G.164, G.165, Q.166, A.191 23 PLIP interactions: 17 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:G.43, C:G.43, C:S.44, C:G.45, C:K.46, C:K.46, C:S.47, C:S.47, C:S.47, C:V.48, C:Q.96, C:Q.96, C:Q.179, C:Q.179, D:R.157, D:R.157, D:S.163, D:G.164, D:Q.166, D:Q.166 Salt bridges: C:K.46 pi-Stacking: C:F.13, C:F.13 AGS.4: 23 residues within 4Å: Chain C: R.146, Q.153, L.154, S.155, G.156, G.157, M.158, A.183 Chain D: Y.22, A.37, E.56, S.57, G.58, C.59, G.60, K.61, S.62, T.63, R.66, Q.106, Q.187, H.220, P.286 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.58, D:G.58, D:C.59, D:G.60, D:K.61, D:K.61, D:S.62, D:T.63, D:R.66, D:R.66, D:Q.106, D:Q.106, D:Q.187, C:R.146, C:R.146, C:S.155, C:S.155, C:G.156 Salt bridges: D:K.61 pi-Stacking: D:Y.22, D:Y.22

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 9 residues within 4Å: Chain C: H.247, P.248, C.284, L.286, C.290, Y.292, C.297, C.315, H.316 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.284, C:C.290, C:C.297, C:C.315 SF4.3: 10 residues within 4Å: Chain D: H.255, P.256, C.293, N.296, C.299, R.301, C.306, C.323, F.324, A.325 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.293, D:C.299, D:C.306, D:C.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, P. et al., Structural characterization of the ABC transporter DppABCDF in Escherichia coli reveals insights into dipeptide acquisition. Plos Biol. (2025)

Release Date

2025-01-29

Peptides

Dipeptide transport system permease protein DppB: A
Dipeptide transport system permease protein DppC: B
Dipeptide transport ATP-binding protein DppD: C
Dipeptide transport ATP-binding protein DppF: D
Dipeptide-binding protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Dipeptide transport system permease protein DppB

Dipeptide transport system permease protein DppC

Dipeptide transport ATP-binding protein DppD

Dipeptide transport ATP-binding protein DppF

Dipeptide-binding protein

Related Entries With Identical Sequence