SMTL ID : 7qba.1

CryoEM structure of the ABC transporter NosDFY complexed with nitrous oxide reductase NosZ

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain B: T.48, E.86, Q.159 Ligands: ATP.2 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.48, B:E.86, B:E.86 MG.3: 5 residues within 4Å: Chain C: T.48, E.86, D.158, Q.159 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.48, C:E.86

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

ATP.2: 22 residues within 4Å: Chain B: Y.18, V.23, H.42, N.43, G.44, A.45, G.46, K.47, T.48, T.49, E.86, Q.159, H.191 Chain C: R.129, T.133, Y.134, S.135, K.136, G.137, M.138, G.163 Ligands: MG.1 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.44, B:A.45, B:G.46, B:G.46, B:K.47, B:T.48, B:T.48, B:T.49, B:T.49, C:R.129, C:R.129, C:S.135, C:K.136, C:G.137, C:G.163 Salt bridges: B:K.47, B:K.47, B:K.47, B:H.191 pi-Stacking: B:Y.18 ATP.4: 22 residues within 4Å: Chain B: R.129, T.133, S.135, K.136, G.137, M.138, G.163 Chain C: Y.18, M.21, V.23, H.42, N.43, G.44, A.45, G.46, K.47, T.48, T.49, E.86, Q.159, H.191 Ligands: MG.3 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:A.45, C:G.46, C:G.46, C:K.47, C:T.48, C:T.48, C:T.49, C:Q.159, B:R.129, B:S.135, B:K.136, B:G.137, B:G.163 Salt bridges: C:K.47, C:K.47, C:H.191 pi-Stacking: C:Y.18, C:Y.18

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain F: Y.256, E.259, M.267, D.273, N.324 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:Y.256, F:E.259, F:M.267, F:D.273, F:D.273 CA.6: 6 residues within 4Å: Chain G: Y.256, S.258, E.259, M.267, D.273, N.324 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:Y.256, G:E.259, G:E.259, G:M.267, G:D.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muller, C. et al., Molecular interplay of an assembly machinery for nitrous oxide reductase. Nature (2022)

Release Date

2022-08-03

Peptides

Probable ABC transporter binding protein NosD: A
Probable ABC transporter ATP-binding protein NosF: BC
Probable ABC transporter permease protein NosY: DE
Nitrous-oxide reductase: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
H

G
I

Membrane

We predict this structure to be a membrane protein.
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Probable ABC transporter binding protein NosD

Probable ABC transporter ATP-binding protein NosF

Probable ABC transporter permease protein NosY

Nitrous-oxide reductase

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