7mdj

The structure of KcsA in complex with a synthetic Fab

Method: X-RAY DIFFRACTION Dmax: 78.6 Å Quality: REASONABLE

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

pH-gated potassium channel KcsA

Streptomyces lividans

UniProt P0A334

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 heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain C; UniProt 1–124 Not recorded Fab heavy chain × 4 Fab light chain × 4 K POTASSIUM ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293 K;50 mM sodium acetate/50 mM ammonium acetate, 50 mM magnesium acetate, 25% PEG 400. Resolution 2.75 Å R-free 0.265

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.

86 other PDB entries and 96 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCSA_STRLI
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–124; UniProt 1–124

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 7mdj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7mdj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7mdj
Deposition date deposition_date2021-04-05
Structure title titleThe structure of KcsA in complex with a synthetic Fab
Keywords keywordsion channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.68
Radius of gyration Rg (electron density) rg_electron30.16
Forward intensity I(0) i048218600.00
Molecular weight molecular_weight55068.0 kDa
Excluded volume excluded_volume69172 ų
Envelope volume envelope_volume90253 ų
Hydration-shell volume shell_volume27857 ų
Envelope diameter envelope_diameter129.0
Shell Rg shell_rg33.27
Envelope Rg envelope_rg31.20
Shape Rg shape_rg30.12
Total Rg total_rg30.58
Total atoms total_atoms3878
Residues n_residues512
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 dmax78.6
Rg (real space) rg_real27.05
Rg uncertainty (real space) rg_real_error0.19
I(0) (real space) i0_real4.5590e+07
I(0) uncertainty (real space) i0_real_error5.2430e+05
Rg (reciprocal space) rg_reciprocal30.00
I(0) (reciprocal space) i0_reciprocal48210000.0000
Solution quality estimate total_estimate0.6862
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.345
Kurtosis Kurtosis kurtosis-0.441
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha1.8520
Highest regularization parameter α highest_alpha4265000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.991; Stabil: 0.984; Sysdev: 0.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7mdjA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7mdjA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7mdjB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7mdjB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)