SMTL ID : 7u8g.1

Cryo-EM structure of the core human NADPH oxidase NOX2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 18 residues within 4Å: Chain A: K.338, L.339, L.340, G.341, S.342, A.343, L.346, L.404, A.407, I.408, I.411, A.412, F.415, W.419, D.429, S.432 Chain B: T.23 Ligands: POV.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.407, A:I.408, A:I.411, A:I.411, A:F.415 Hydrogen bonds: A:S.342 pi-Cation interactions: A:W.419 POV.2: 22 residues within 4Å: Chain A: W.400, A.403, S.406, A.407, T.410, I.411, L.414, T.477, L.480, I.481, I.484, T.485, T.488, K.489 Chain B: L.15, A.16, L.19, I.20, T.23, G.24, A.106, L.109 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.400, A:A.407, A:T.410, A:L.414, A:T.477, A:I.481, A:I.481, A:I.484, B:A.16, B:L.19, B:L.109 Hydrogen bonds: A:K.489 POV.8: 10 residues within 4Å: Chain A: I.411, F.415, W.419 Chain B: T.23, I.26, V.27, A.30, G.31, R.32 Ligands: POV.1 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.415, B:I.26, B:V.27, B:A.30

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

NAG.3: 4 residues within 4Å: Chain A: L.530, N.534, T.536, V.537 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.534 NAG.4: 2 residues within 4Å: Chain A: Q.442, N.443 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.443 NAG.5: 1 residues within 4Å: Chain A: N.426 No protein-ligand interaction detected (PLIP)

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

HEM.6: 26 residues within 4Å: Chain A: I.361, L.362, V.365, R.367, L.392, H.395, K.396, A.399, W.400, I.402, L.480, I.483, I.484, S.487, R.492, F.496, F.499, W.500, H.503, H.504, F.506, F.509, F.510, Y.574, R.578, R.581 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:L.362, A:V.365, A:L.392, A:A.399, A:L.480, A:I.483, A:I.484, A:F.499, A:F.506, A:F.506, A:F.510, A:Y.574 Hydrogen bonds: A:W.500, A:Y.574 Salt bridges: A:R.367, A:R.578, A:R.581 pi-Stacking: A:F.499 Metal complexes: A:H.395 HEM.7: 27 residues within 4Å: Chain A: R.348, A.351, L.354, N.355, C.358, I.402, S.406, H.409, T.410, H.413, A.469, G.470, G.473, V.474, I.476, T.477, L.480, F.509, L.513, H.516, G.517, R.520, I.521, V.522, P.561, M.562, T.563 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.354, A:L.354, A:T.410, A:A.469, A:I.476, A:I.476, A:F.509, A:L.513, A:I.521 Hydrogen bonds: A:G.517, A:R.520, A:I.521, A:V.522, A:M.562, A:T.563 pi-Stacking: A:H.413 Metal complexes: A:H.516

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noreng, S. et al., Structure of the core human NADPH oxidase NOX2. Nat Commun (2022)

Release Date

2022-10-26

Peptides

EGFP, Cytochrome b-245 heavy chain chimera: A
Cytochrome b-245 light chain: B
7G5 - heavy chain: C
7G5 - light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

Membrane

We predict this structure to be a membrane protein.
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EGFP, Cytochrome b-245 heavy chain chimera

Cytochrome b-245 light chain

7G5 - heavy chain

7G5 - light chain

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