5tfd

Nucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with CTP

Method: X-RAY DIFFRACTION Dmax: 62.0 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cystic fibrosis transmembrane conductance regulator

Homo sapiens

UniProt P13569

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 387–646 Fragment:Nucleotide-binding domain 1 (UNP residues 387-646) Mutation:V470M MG MAGNESIUM ION × 1 CTP CYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;279 K;Protein buffer: 150 mM NaCl, 30% (v/v) glycerol, 1 mM TCEP, and 20 mM Na-HEPES, pH 7.5; Precipitant buffer: 40% (v/v) PEG 400, 100 mM NH4Cl, and 100 mM MES, pH 6 Resolution 1.89 Å R-free 0.195

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.

52 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CFTR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–229; UniProt 387–646

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 5tfd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tfd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tfd
Deposition date deposition_date2016-09-24
Structure title titleNucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with CTP
Keywords keywordshNBD1, CFTR, ABC transport, ATP, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.86
Radius of gyration Rg (electron density) rg_electron17.90
Forward intensity I(0) i010345100.00
Molecular weight molecular_weight24022.0 kDa
Excluded volume excluded_volume30112 ų
Envelope volume envelope_volume34263 ų
Hydration-shell volume shell_volume16450 ų
Envelope diameter envelope_diameter61.9
Shell Rg shell_rg23.48
Envelope Rg envelope_rg18.20
Shape Rg shape_rg17.94
Total Rg total_rg18.64
Total atoms total_atoms1681
Residues n_residues215
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax62.0
Rg (real space) rg_real18.83
Rg uncertainty (real space) rg_real_error0.33
I(0) (real space) i0_real1.0350e+07
I(0) uncertainty (real space) i0_real_error1.3070e+05
Rg (reciprocal space) rg_reciprocal18.83
I(0) (reciprocal space) i0_reciprocal10350000.0000
Solution quality estimate total_estimate0.8872
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary21.5
Skewness Skewness skewness0.327
Kurtosis Kurtosis kurtosis-0.311
Angular range angular_range— – 0.4200 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha1932000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5tfda_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like

CATH v4.4 (1 domains)

Domain ID domain_id5tfdA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)