Phase 6C · Actual deposited atom evidence

Experimental structure quality

Which PWWP regions have observed heavy atoms and experimentally defined ligand environments? Inspect the provenance, missing residues, and local contact limitations without generating receptor models or binding predictions.

666Chain/domain inventory rows

22Locally parsed coordinate records

4Experimental research-ligand environments

644All-atom assessment not possible here

Authoritative experimental observations

Source-supported pocket context

Export measured local environments

6G2O · NSD3 PWWP1

Observed EJE environment

One source-tagged experimental research ligand and a locally complete observed annotation core. Residue/ligand contacts are independently recalculated.

Inspect 6G2O atomic assessment

6XCG · NSD2 PWWP1

Three V01 ligand instances

Distinct deposited ligand instances and protein chains are retained. Local alternative-conformer and partial-occupancy annotations are visible separately.

Inspect 6XCG atomic assessment

11OA · DNMT3A PWWP1

Side-chain coordinate gap

Five observed cores contain 990 missing standard side-chain heavy atoms. Thirteen other mapped chains have no observed PWWP-core coordinates.

Inspect 11OA atom evidence

Directly calculated from the bundled coordinates

Measured structural differences

Observed PWWP core missing side-chain heavy atoms, 6G2O zero, 6XCG 4 to 12 and five 11OA cores each 198. — Missing heavy-atom evidence among observed residues; no-core chains are not treated as complete.

Line plot comparing distinct residue contacts across 3.5, 4, 5 and 6 angstrom distance thresholds for four deposited ligand instances. — Simple geometric proximity and sensitivity, not a hydrogen-bond, density-fit or affinity assessment.

All 666 chain/domain records

Structural-quality inventory

Full inventory CSV Assessment CSV

Protein, PDB or domain Protein Domain Processing outcome Observed-core finding Ligand environment

Clear filters

4 matching chain/domain records. Filters apply to the same assessed row, not a mixture of unrelated structures. Displaying up to 100 records per page.

PDB / label chain	Protein/domain	Core Cα	Original experiment	Observed missing side-chain atoms	Processing	Receptor assessment
9E3D · S	DNMT3B PWWP1	0 / 59	ELECTRON MICROSCOPY · 3.8 Å	Not assessed	coordinates not packaged	not assessed
9E3D · T	DNMT3B PWWP1	0 / 59	ELECTRON MICROSCOPY · 3.8 Å	Not assessed	coordinates not packaged	not assessed
9E3D · U	DNMT3A PWWP1	0 / 59	ELECTRON MICROSCOPY · 3.8 Å	Not assessed	coordinates not packaged	not assessed
9E3D · V	DNMT3A PWWP1	59 / 59	ELECTRON MICROSCOPY · 3.8 Å	Not assessed	coordinates not packaged	not assessed

Methods, receptor qualifications & downloads

One independent Gemmi parse checked first-model experimental protein atoms against the earlier Biopython results. Atom-name completeness uses the mmCIF's own standard amino-acid component definitions, excludes hydrogens, and never interprets missing coordinates as chemical inactivity. Ligand–residue geometric contacts use a declared 5 Å primary cutoff with sensitivity analyses, and are not hydrogen bonds, binding energies or density validation.

Residue and missing-atom table Atom-pair distance evidence 11OA audit Source hashes and methods