SMTL ID : 8x2l.1

Structure of human phagocyte NADPH oxidase in the resting state in the presence of 2 mM NADPH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain B: N.149 Chain C: T.80, H.82 Chain D: L.117 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.80

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 21 residues within 4Å: Chain B: R.199, S.200, Y.201, F.202, E.203, Y.324, W.337, H.338, P.339, F.340, T.341, H.354, I.355, R.356, V.358, G.359, D.360, W.361, T.362, T.414 Ligands: MG.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.324, B:P.339 Hydrogen bonds: B:S.200, B:F.202, B:E.203, B:W.337, B:H.338, B:P.339, B:T.341, B:T.341, B:H.354, B:R.356, B:D.360, B:W.361, B:T.362 Salt bridges: B:H.338 pi-Stacking: B:F.202, B:F.340

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

HEM.3: 24 residues within 4Å: Chain A: L.109 Chain B: R.54, A.57, L.60, N.61, S.112, H.115, T.116, H.119, A.175, G.179, I.182, T.183, F.215, L.219, H.222, G.223, E.225, R.226, I.227, V.228, P.267, M.268, T.269 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:A.57, B:L.60, B:T.116, B:A.175, B:I.182, B:I.182, B:F.215, B:I.227, B:V.228, A:L.109 Hydrogen bonds: B:N.61, B:E.225, B:R.226, B:I.227, B:V.228, B:M.268, B:T.269, B:T.269 Salt bridges: B:R.54 pi-Cation interactions: B:H.119 Metal complexes: B:H.115, B:H.222 HEM.4: 21 residues within 4Å: Chain B: I.67, L.68, V.71, L.98, H.101, K.102, A.105, L.186, I.189, I.190, S.193, R.198, F.202, F.205, W.206, H.209, F.212, F.215, F.216, Y.280, R.287 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:I.67, B:L.68, B:V.71, B:V.71, B:V.71, B:L.98, B:L.98, B:K.102, B:L.186, B:I.190, B:F.205, B:F.212, B:F.212, B:F.215, B:F.216 Hydrogen bonds: B:V.71, B:R.284 Salt bridges: B:R.73, B:R.287 pi-Stacking: B:F.205 Metal complexes: B:H.101

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 3 residues within 4Å: Chain B: N.132 Chain D: Y.73, S.75 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:N.132, D:S.75 Hydrophobic interactions: D:Y.73 NAG.6: 3 residues within 4Å: Chain B: N.240, T.242, V.243 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain B: E.203, D.360 Ligands: FAD.2 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.203, B:D.360

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Structure of human phagocyte NADPH oxidase in the activated state. Nature (2024)

Release Date

2024-01-24

Peptides

Cytochrome b-245 light chain: A
Cytochrome b-245 heavy chain: B
7D5 Fab heavy chain: C
7D5 Fab light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-245 light chain

Cytochrome b-245 heavy chain

7D5 Fab heavy chain

7D5 Fab light chain

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