SMTL ID : 8gz3.1

Structure of human phagocyte NADPH oxidase in the resting state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-1-1-1-1-1-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: 3 residues within 4Å: Chain B: Q.148, N.149 Chain D: X.57 No protein-ligand interaction detected (PLIP)

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

FAD.2: 18 residues within 4Å: Chain B: R.199, S.200, F.202, 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 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.324, B:P.339 Hydrogen bonds: B:S.200, B:F.202, B:W.337, B:H.338, B:P.339, B:T.341, B:T.341, B:H.354, B:R.356, B:R.356, B:D.360, B:D.360, B:W.361, B:T.362, 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: 22 residues within 4Å: Chain B: 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 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:A.57, B:L.60, B:T.116, B:H.119, B:A.175, B:I.182, B:I.182, B:F.215, B:I.227, B:V.228 Hydrogen bonds: B:E.225, B:R.226, B:I.227, B:V.228, B:M.268, B:T.269, B:T.269 pi-Stacking: B:H.119 Metal complexes: B:H.115, B:H.222 HEM.4: 20 residues within 4Å: Chain B: I.67, L.68, V.71, L.98, H.101, K.102, A.105, 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 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:I.67, B:I.67, B:L.68, B:V.71, B:V.71, B:V.71, B:L.98, B:K.102, B:I.189, B:I.190, B:F.205, B:F.212, B:F.212, B:F.215, B:F.216, B:Y.280 Hydrogen bonds: B:V.71 Salt bridges: B:R.284, B:R.287 pi-Stacking: B:F.205 Metal complexes: B:H.101, B:H.209

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

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

1 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.7: 15 residues within 4Å: Chain A: I.22, T.23, I.26, A.30, G.31 Chain B: K.44, L.45, G.47, S.48, A.49, L.52, I.114, I.117, F.121, W.125 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.22, A:T.23, A:I.26, A:A.30, B:L.52, B:I.114, B:I.117, B:I.117, B:F.121, B:F.121 Hydrogen bonds: B:S.48 pi-Cation interactions: B:W.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, R. et al., Structure of human phagocyte NADPH oxidase in the resting state. Elife (2022)

Release Date

2022-12-21

Peptides

Cytochrome b-245 light chain: A
Cytochrome b-245 heavy chain: B
7D5 Fab light chain: C
7D5 Fab heavy chain: D
Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
L

D
H

E
N

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 light chain

7D5 Fab heavy chain

Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera

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