SMTL ID : 7zdu.1

Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC)/ATP(CydD) bound state (Dataset-19)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.380, Q.421 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.380 MG.3: 3 residues within 4Å: Chain B: S.390, Q.430 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.390

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

ATP.2: 19 residues within 4Å: Chain A: Y.348, Q.351, T.375, G.376, C.377, G.378, K.379, S.380, T.381, Q.421, Q.500, H.531 Chain B: A.484, R.485, S.487, G.489, Q.490, S.515 Ligands: MG.1 23 PLIP interactions: 15 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:G.376, A:G.376, A:C.377, A:G.378, A:K.379, A:S.380, A:T.381, A:T.381, A:Q.421, A:Q.500, B:A.484, B:R.485, B:R.485, B:S.487, B:V.488, B:G.489, B:Q.490, B:Q.490 Salt bridges: A:K.379, A:K.379, A:H.531 pi-Stacking: A:Y.348, A:Y.348 ATP.4: 20 residues within 4Å: Chain A: K.457, R.473, Q.474, S.476, G.477, G.478, E.479 Chain B: S.359, E.361, L.365, R.384, S.385, G.386, S.387, G.388, K.389, S.390, S.391, Q.430 Ligands: MG.3 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:R.473, A:Q.474, A:S.476, A:G.477, A:G.478, A:E.479, B:E.361, B:G.386, B:G.386, B:S.387, B:G.388, B:K.389, B:S.390, B:S.391, B:Q.430, B:Q.430 Salt bridges: B:K.389, 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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