SMTL ID : 8z1x.1

Cryo-EM structure of Escherichia coli DppBCDF complex bound to AMPPNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

SF4.1: 9 residues within 4Å: Chain C: P.248, C.284, L.286, N.287, 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: 9 residues within 4Å: Chain D: H.255, 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

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 13 residues within 4Å: Chain D: Y.22, V.35, A.37, E.56, S.57, G.58, C.59, G.60, K.61, S.62, T.63, R.66, P.286 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.57, D:G.58, D:C.59, D:G.60, D:K.61, D:K.61, D:S.62, D:S.62, D:T.63, D:R.66 pi-Stacking: D:Y.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, P. et al., Cryo-EM structure of Escherichia coli DppBCDF complex bound to AMPPNP. To Be Published

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

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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Dipeptide transport system permease protein DppB

Dipeptide transport system permease protein DppC

Dipeptide transport ATP-binding protein DppD

Dipeptide transport ATP-binding protein DppF

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