SMTL ID : 8wej.1

Structure of human phagocyte NADPH oxidase in the activated state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-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: 5 residues within 4Å: Chain B: Q.148, N.149 Chain F: T.80, H.82 Chain G: L.117 No protein-ligand interaction detected (PLIP)

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

HEM.2: 25 residues within 4Å: Chain A: L.109 Chain B: R.54, A.57, L.60, N.61, C.64, 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 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:A.57, B:L.60, B:L.60, B:L.60, B:T.116, B:A.175, B:I.182, B:I.182, B:T.183, B:F.215, B:I.227, B:I.227, A:L.109 Hydrogen bonds: B:R.54, B:N.61, B:R.226, B:I.227, B:V.228, B:M.268, B:T.269 pi-Stacking: B:H.119 Metal complexes: B:H.115, B:H.222 HEM.3: 22 residues within 4Å: Chain B: I.67, L.68, V.71, R.73, 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.284 27 PLIP interactions: 27 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:K.102, B:A.105, B:L.186, B:I.189, B:I.190, B:F.212, B:F.212, B:F.215, B:F.216 Hydrogen bonds: B:W.206, B:Y.280, B:Y.280 Salt bridges: B:R.73, B:R.73, B:H.210, B:R.284, B:R.287 pi-Stacking: B:H.101, B:F.205, B:H.209 Metal complexes: B:H.101

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

NAG.4: 2 residues within 4Å: Chain B: N.132 Chain G: S.75 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:N.132, G:S.75 NAG.5: 2 residues within 4Å: Chain B: N.240, V.243 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.240

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain B: D.360 Ligands: FDA.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.360, FDA.8 MG.10: 5 residues within 4Å: Chain E: T.17, T.35, D.57, T.58 Ligands: GTP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.17, E:T.35

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.7: 19 residues within 4Å: Chain B: R.356, A.409, G.410, I.411, L.444, C.445, R.446, T.481, R.513, W.516, C.537, G.538, P.539, A.541, L.542, T.545, E.568, N.569, F.570 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.570 Hydrogen bonds: B:I.411, B:L.444, B:T.481, B:R.513, B:T.545, B:T.545, B:F.570 Salt bridges: B:R.356, B:R.446, B:R.446, B:R.513 pi-Cation interactions: B:R.513, B:R.513

1 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.8: 22 residues within 4Å: Chain B: R.198, R.199, 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, I.411, T.414, N.569, F.570 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.324, B:P.339 Hydrogen bonds: B:R.198, B:W.337, 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.202, B:F.340, B:F.570, B:F.570

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.9: 25 residues within 4Å: Chain E: D.11, G.12, A.13, V.14, G.15, K.16, T.17, C.18, F.28, G.30, Y.32, I.33, P.34, T.35, T.58, A.59, G.60, L.61, K.116, D.118, L.119, S.158, A.159, L.160 Ligands: MG.10 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:A.13, E:V.14, E:G.15, E:K.16, E:T.17, E:T.17, E:T.17, E:C.18, E:T.35, E:G.60, E:K.116, E:S.158, E:A.159, E:L.160 Salt bridges: E:K.16, E:K.16, E:D.118 pi-Stacking: E:F.28, E:F.28

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
Neutrophil cytosol factor 1: C
Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a: D
Rac family small GTPase 1: E
7D5 Fab heavy chain: F
7D5 Fab light chain: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
H

G
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

Neutrophil cytosol factor 1

Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a

Rac family small GTPase 1

7D5 Fab heavy chain

7D5 Fab light chain

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