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3a1f

The crystal structure of NADPH binding domain of gp91(phox)

Method: X-RAY DIFFRACTION Dmax: 55.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome b-245 heavy chain

Homo sapiens

UniProt P04839

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 385–570 Fragment：UNP residues 385-570 NI NICKEL (II) ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；12% PEG 3350, 0.1M sodium acetate pH 5.6, 0.4M NiCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.00 Å R-free 0.277

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3A1F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7U8G Cryo-EM structure of the core human NADPH oxidase NOX2 Deposited 2022-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–570（569 aa） Fragment：N-terminal 2x streptag followed by EGFP and TEV + thrombin cleavage sites.
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；0.03% DDM, 150 mM NaCl, 20 mM Tris
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8GZ3 Structure of human phagocyte NADPH oxidase in the resting state Deposited 2022-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–570（570 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8KEI Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS Deposited 2023-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 6–570（565 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
8WEJ Structure of human phagocyte NADPH oxidase in the activated state Deposited 2023-09-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–570（570 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
8X2L Structure of human phagocyte NADPH oxidase in the resting state in the presence of 2 mM NADPH Deposited 2023-11-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–570（570 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CY24B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–186； UniProt 385–570

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3a1f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3a1f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3a1f
Deposition date deposition_date2009-04-01
Structure title titleThe crystal structure of NADPH binding domain of gp91(phox)
Keywords keywordsgp91(phox), NADPH binding domain, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.02 Å
Radius of gyration Rg (electron density) rg_electron15.34 Å
Forward intensity I(0) i06507560.00
Molecular weight molecular_weight18423.0 kDa
Excluded volume excluded_volume22908 ų
Envelope volume envelope_volume25753 ų
Hydration-shell volume shell_volume14236 ų
Envelope diameter envelope_diameter55.4 Å
Shell Rg shell_rg21.28 Å
Envelope Rg envelope_rg15.65 Å
Shape Rg shape_rg15.21 Å
Total Rg total_rg16.80 Å
Total atoms total_atoms1284
Residues n_residues163
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax55.9 Å
Rg (real space) rg_real16.90 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real6.5080e+06
I(0) uncertainty (real space) i0_real_error8.4090e+04
Rg (reciprocal space) rg_reciprocal16.91 Å
I(0) (reciprocal space) i0_reciprocal6508000.0000
Solution quality estimate total_estimate0.7164
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.3 Å
Skewness Skewness skewness0.087
Kurtosis Kurtosis kurtosis-0.376
Angular range angular_range— – 0.4700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1086000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 0.322; Positv: 1.000; Valcen: 0.998; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3a1fA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
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8. Citations (1)

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9. Files and Curves (10)