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4k6j

Human cohesin inhibitor WapL

Method: X-RAY DIFFRACTION Dmax: 107.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Wings apart-like protein homolog

Homo sapiens

UniProt Q7Z5K2

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 631–1190 Fragment：Wapl C-terminal domain (UNP Residues 631-1190) SO4 SULFATE ION × 7 ACT ACETATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；1.4 M ammonium sulfate, 0.1 M HEPES pH 7.1, 10% glycerol, vapor diffusion, sitting drop, temperature 293K Resolution 2.62 Å R-free 0.237
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 631–1190 Fragment：Wapl C-terminal domain (UNP Residues 631-1190) SO4 SULFATE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；1.4 M ammonium sulfate, 0.1 M HEPES pH 7.1, 10% glycerol, vapor diffusion, sitting drop, temperature 293K Resolution 2.62 Å R-free 0.237

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 4K6J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5HDT Human cohesin regulator Pds5B bound to a Wapl peptide Deposited 2016-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 44–76（33 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2 M Sodium Citrate and 20% PEG3350 (vol/vol) without buffer or with buffer 0.1 M Bis-Tris propane pH6.5, pH 7.5 or pH 8.5
Resolution 2.71 Å R-free 0.253
9EP3 Structure of the SA2/SCC1/WAPL complex Deposited 2024-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 547–568（22 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K
Resolution 3.08 Å R-free 0.268

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WAPL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–568； UniProt 631–1190 Author chain B； PDBConstruct 9–568； UniProt 631–1190

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 4k6j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4k6j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4k6j
Deposition date deposition_date2013-04-16
Structure title titleHuman cohesin inhibitor WapL
Keywords keywordsheat repeats, cohesin regulator, Cell Adhesion Inhibitor, cell cycle, nuclear protein, protein-binding; CELL CYCLE
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_guinier34.05 Å
Radius of gyration Rg (electron density) rg_electron33.33 Å
Forward intensity I(0) i0205895000.00
Molecular weight molecular_weight110750.0 kDa
Excluded volume excluded_volume137120 ų
Envelope volume envelope_volume185410 ų
Hydration-shell volume shell_volume45508 ų
Envelope diameter envelope_diameter116.0 Å
Shell Rg shell_rg40.72 Å
Envelope Rg envelope_rg33.17 Å
Shape Rg shape_rg33.34 Å
Total Rg total_rg33.88 Å
Total atoms total_atoms15451
Residues n_residues968
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 dmax107.2 Å
Rg (real space) rg_real33.92 Å
Rg uncertainty (real space) rg_real_error0.76 Å
I(0) (real space) i0_real2.0590e+08
I(0) uncertainty (real space) i0_real_error3.1970e+06
Rg (reciprocal space) rg_reciprocal34.00 Å
I(0) (reciprocal space) i0_reciprocal205900000.0000
Solution quality estimate total_estimate0.6841
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.3 Å
Skewness Skewness skewness0.161
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32880000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.995; Smooth: 0.946
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4k6jA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id4k6jB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
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8. Citations (2)

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9. Files and Curves (10)