5vkh

Closed conformation of KcsA Y82A-F103A mutant

Method: X-RAY DIFFRACTION Dmax: 126.5 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 22–124 Not recorded Antibody Heavy Chain × 4 Antibody Light Chain × 4 F09 NONAN-1-OL × 4 1EM (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE × 4 K POTASSIUM ION × 24 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;PEG400 , 50 mM magnesium acetate, 50 mM sodium acetate Resolution 2.25 Å R-free 0.203

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 1–103; UniProt 22–124

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 5vkh

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5vkh
Deposition date deposition_date2017-04-21
Structure title titleClosed conformation of KcsA Y82A-F103A mutant
Keywords keywordsKcsA, closed, Y82A-F103A, potassium channel, IMMUNE SYSTEM-TRANSPORT PROTEIN complex; IMMUNE SYSTEM/TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.96
Radius of gyration Rg (electron density) rg_electron30.57
Forward intensity I(0) i052742400.00
Molecular weight molecular_weight58067.0 kDa
Excluded volume excluded_volume73012 ų
Envelope volume envelope_volume93560 ų
Hydration-shell volume shell_volume28269 ų
Envelope diameter envelope_diameter130.3
Shell Rg shell_rg33.97
Envelope Rg envelope_rg31.59
Shape Rg shape_rg30.53
Total Rg total_rg31.04
Total atoms total_atoms4083
Residues n_residues534
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 dmax126.5
Rg (real space) rg_real30.60
Rg uncertainty (real space) rg_real_error1.92
I(0) (real space) i0_real5.2740e+07
I(0) uncertainty (real space) i0_real_error9.9060e+05
Rg (reciprocal space) rg_reciprocal30.32
I(0) (reciprocal space) i0_reciprocal52730000.0000
Solution quality estimate total_estimate0.6912
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.964
Kurtosis Kurtosis kurtosis1.070
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7584000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.272; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.217; Smooth: 0.948

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd5vkha1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5vkha2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd5vkha3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5vkhb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5vkhb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd5vkhc_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.14 — Gated ion channels
Superfamily Superfamily superfamilyf.14.1 — Voltage-gated ion channels
Family Family familyf.14.1.1 — Voltage-gated potassium channels

CATH v4.4 (4 domains)

Domain ID domain_id5vkhA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5vkhB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5vkhB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5vkhC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70

8. Citations (1)

9. Files and Curves (10)