SMTL ID : 6qq6.1

Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) Val495Ala mutant from Alcaligenes xylosoxidans

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)(Covalent)

HEM.1: 27 residues within 4Å: Chain A: G.76, A.77, Y.78, Q.79, Q.296, V.297, G.300, G.301, T.303, A.304, Y.324, R.328, H.331, I.332, A.335, I.339, E.407, Y.408, A.630, H.631, L.634, F.635, R.720, D.724, F.727 Ligands: HEM.2, CA.4 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:V.297, A:T.303, A:I.332, A:I.332, A:A.335, A:I.339, A:Y.408, A:A.630, A:L.634, A:L.634, A:F.635, A:F.635, A:F.727, A:F.727 Hydrogen bonds: A:Y.78, A:Y.324, A:Y.408 Salt bridges: A:R.328, A:R.328 Metal complexes: A:H.331, A:H.631 HEM.2: 27 residues within 4Å: Chain A: H.75, Y.78, E.407, Y.408, W.482, E.490, H.537, H.538, S.556, E.559, V.560, L.563, N.600, A.604, G.608, I.611, N.612, L.617, Q.621, T.626, H.629, A.630, A.633, L.634, Y.638 Ligands: HEM.1, CA.4 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.408, A:W.482, A:E.490, A:V.560, A:L.563, A:I.611, A:I.611, A:N.612, A:L.617, A:L.617, A:A.630, A:A.633, A:L.634 Hydrogen bonds: A:Y.408, A:Q.621, A:G.622, A:T.626, A:T.626 Salt bridges: A:H.75 pi-Stacking: A:H.538 Metal complexes: A:H.629, H2O.1 HEM.6: 27 residues within 4Å: Chain B: G.76, A.77, Y.78, Q.79, Q.296, V.297, G.300, G.301, T.303, A.304, Y.324, R.328, H.331, I.332, A.335, I.339, E.407, Y.408, A.630, H.631, L.634, F.635, R.720, D.724, F.727 Ligands: HEM.7, CA.9 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:V.297, B:T.303, B:A.304, B:I.332, B:I.332, B:A.335, B:I.339, B:Y.408, B:A.630, B:L.634, B:L.634, B:F.635, B:F.635, B:F.727, B:F.727 Hydrogen bonds: B:Y.78, B:Y.324, B:Y.408 Salt bridges: B:R.328, B:R.328 Metal complexes: B:H.331, B:H.631 HEM.7: 27 residues within 4Å: Chain B: H.75, Y.78, E.407, Y.408, W.482, E.490, H.537, H.538, S.556, E.559, V.560, L.563, N.600, A.604, G.608, I.611, N.612, L.617, Q.621, T.626, H.629, A.630, A.633, L.634, Y.638 Ligands: HEM.6, CA.9 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.408, B:W.482, B:E.490, B:V.560, B:L.563, B:I.611, B:I.611, B:N.612, B:L.617, B:L.617, B:A.630, B:A.633, B:L.634 Hydrogen bonds: B:Y.408, B:Q.621, B:T.626, B:T.626 Salt bridges: B:H.75 pi-Stacking: B:H.538 Metal complexes: B:H.629, H2O.1

2 x FE: FE (III) ION(Non-covalent)

FE.3: 3 residues within 4Å: Chain A: H.486, H.537, H.538 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.486, A:H.537, A:H.538, H2O.1 FE.8: 3 residues within 4Å: Chain B: H.486, H.537, H.538 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.486, B:H.537, B:H.538, H2O.1

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: G.76, Y.78, E.407 Ligands: HEM.1, HEM.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.76, A:Y.78, A:E.407 CA.9: 5 residues within 4Å: Chain B: G.76, Y.78, E.407 Ligands: HEM.6, HEM.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.76, B:Y.78, B:E.407

3 x LOP: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

LOP.5: 9 residues within 4Å: Chain A: F.680, T.681, P.685, L.688, I.689, H.692, I.712 Chain B: M.231 Ligands: LOP.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.680, A:P.685, A:P.685, A:I.689, A:I.712 Salt bridges: A:H.692 LOP.10: 13 residues within 4Å: Chain A: F.598, F.680, L.688 Chain B: I.235, V.238, V.239, A.242, L.246, W.249, A.250, F.253, L.254 Ligands: LOP.5 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.598, A:F.680, A:L.688, B:I.235, B:V.239, B:A.242, B:A.250, B:L.254 LOP.11: 7 residues within 4Å: Chain A: M.231 Chain B: F.680, P.685, L.688, I.689, H.692, I.712 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.680, B:P.685, B:L.688, B:L.688, B:I.689, B:I.712 Salt bridges: B:H.692, B:H.692

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.12: 11 residues within 4Å: Chain A: H.224, P.225, S.226, S.227, V.230, V.615 Chain B: V.615, Y.619, V.695, S.696 Ligands: LMT.13 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.230, A:V.615, A:V.615, B:V.615, B:Y.619, B:V.695 Hydrogen bonds: A:S.226, B:Y.619, B:Y.619, B:V.695 Salt bridges: A:H.224 LMT.13: 15 residues within 4Å: Chain A: P.219, V.615, S.616, Y.619, V.695, S.696, E.697 Chain B: H.224, P.225, S.226, S.227, V.230, S.233, V.615 Ligands: LMT.12 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.615, A:Y.619, A:V.695, B:V.230, B:V.615 Hydrogen bonds: A:Y.619, B:S.227 Salt bridges: B:H.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gopalasingam, C.C. et al., Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy. Sci Adv (2019)

Release Date

2019-09-11

Peptides

Nitric oxide reductase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Nitric oxide reductase subunit B