SMTL ID : 7zdc.1

IF(heme/confined) conformation of CydDC in ADP(CydD) bound state (Dataset-3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x HEB: HEME B/C(Non-covalent)

HEB.1: 20 residues within 4Å: Chain A: R.81, H.85, T.88, F.89, D.131, H.132, L.135, R.136 Chain B: N.191, N.194, F.195, L.198, T.239, L.243, F.247, S.250, G.308, T.309, Y.311, H.312 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain A, Hydrophobic interactions: B:N.191, B:N.194, B:F.195, B:L.198, B:T.239, B:L.243, B:Y.311, B:Y.311, A:F.89, A:F.89, A:L.135 pi-Stacking: B:F.195, B:F.247, B:H.312, B:H.312, A:H.85 pi-Cation interactions: B:H.312 Metal complexes: B:H.312 Salt bridges: A:R.81, A:R.81

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: S.390, Q.430 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.390

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 13 residues within 4Å: Chain B: A.112, S.359, K.363, L.365, R.384, S.385, G.386, S.387, G.388, K.389, S.390, S.391 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.112, B:S.359, B:K.363, B:S.385, B:G.386, B:S.387, B:G.388, B:K.389, B:S.390, B:S.391, B:S.391 Salt bridges: B:K.389

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, D. et al., Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nat.Chem.Biol. (2023)

Release Date

2023-04-19

Peptides

ATP-binding/permease protein CydC: A
ATP-binding/permease protein CydD: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Membrane

We predict this structure to be a membrane protein.
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ATP-binding/permease protein CydC

ATP-binding/permease protein CydD

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