SMTL ID : 8ipr.1 (1 other biounit)

Cryo-EM structure of heme transporter CydDC from Mycobacterium smegmatis in the outward facing ATP bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.348, D.454 Chain B: L.439 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.348 MG.3: 3 residues within 4Å: Chain B: S.343, H.384 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.343, B:H.384

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 22 residues within 4Å: Chain A: D.108, R.321, R.323, P.324, P.342, S.343, G.344, S.345, G.346, K.347, T.348, T.349, Q.455, H.490 Chain B: E.421, G.436, L.437, S.438, L.439, G.440, Q.441 Ligands: MG.1 21 PLIP interactions: 13 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:D.108, A:S.345, A:G.346, A:G.346, A:K.347, A:T.348, A:T.349, A:Q.455, B:G.436, B:S.438, B:S.438, B:L.439, B:G.440, B:Q.441, B:Q.441, B:H.466 Salt bridges: A:R.323, A:K.347, A:K.347, A:H.490 pi-Cation interactions: A:R.323 ATP.4: 19 residues within 4Å: Chain A: W.411, A.428, A.429, V.430, S.431, A.432, G.433, Q.434 Chain B: R.91, N.338, G.339, V.340, G.341, K.342, S.343, T.344, H.384, P.515 Ligands: MG.3 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.91, B:N.338, B:G.339, B:K.342, B:S.343, B:T.344, B:P.515, A:S.431, A:A.432, A:G.433, A:Q.434, A:Q.434, A:Q.434 Salt bridges: B:K.342, B:K.342 pi-Cation interactions: B:R.91, B:R.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, C. et al., Cryo-EM structures of a prokaryotic heme transporter CydDC. Protein Cell (2023)

Release Date

2023-06-14

Peptides

Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC: A
Transmembrane ATP-binding protein ABC transporter cydD: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Membrane

We predict this structure to be a membrane protein.
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Component linked with the assembly of cytochrome' ABC transporter ATP-binding protein CydC

Transmembrane ATP-binding protein ABC transporter cydD

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