PWWPAtlas
STRUCTURAL BIOLOGY & CHEMICAL EVIDENCEDataset v1.2 · Phase 6D · Comparative experimental recognition environments

Protein record

HDGFL3

Hepatoma-derived growth factor-related protein 3

Q9Y3E1 at UniProt
Homo sapiens203 amino acidsannotation supported
1annotated core in HDGFL3
5PDB entries with observed PWWP1 coordinates
1model records for PWWP1
1frozen v1.2 assay / association records for PWWP1

Canonical sequence · Source-mapped regions

Protein domain architecture

203 residues

PWWP annotation cores, other annotated regions, and deposited construct mappings share the canonical amino acid axis. The original Atlas PWWP intervals retain their source definitions.

PWWP annotation cores PWWP1 · 11–68 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket Other source annotations No additional eligible domain features in the retrieved source. 1 51 102 152 203
PWWP annotation coreOther source annotationPredicted candidate, when present
0 additional source-supported regions · coordinates and evidence

UniProt feature coordinates accepted after exact canonical sequence identity check against the frozen Atlas. Source annotations can be inferred by sequence or curated from experiments; evidence codes remain attached. Other domain types link to their UniProt source because the Atlas records PWWP domains.

Deposited construct mapping

2 selected examples

Colored segments map deposited polymer sequences to this canonical protein; dark segments have observed coordinates. Unmapped tags and engineered residues are not assigned canonical positions. These are not certified whole-fold boundaries.

6IIPchain A8–94
Mapped deposited segment 8–94 Observed canonical residues 8–94
Mapping and construct evidence

Deposited polymer length: 88 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 58 / 58 annotation-core Cα residues observed.

Frozen SIFTS aligned regions with construct-to-UniProt sequence comparison. Bars are mapped canonical segments; tags, insertions, and unmapped termini are not assigned canonical positions. PDB source.

Unmapped construct positions: 1–1.

6IIQchain A1–99
Mapped deposited segment 1–99 Observed canonical residues 1–99
Mapping and construct evidence

Deposited polymer length: 100 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 58 / 58 annotation-core Cα residues observed.

Frozen SIFTS aligned regions with construct-to-UniProt sequence comparison. Bars are mapped canonical segments; tags, insertions, and unmapped termini are not assigned canonical positions. PDB source.

Unmapped construct positions: 1–1.

One mapped example per native domain, preferring frozen experimental representatives; up to four distinct mapped intervals.

Validated isoform differences · 0 PWWP correspondence records

Only source-validated PWWP core correspondences from the frozen v1.2 isoform audit; other-domain architectures are not projected onto isoforms. Coordinates in the isoform column refer to the individual isoform sequence; deleted cores remain absent.

No source-validated alternative-isoform core mapping is available in this snapshot.

Viewing HDGFL3 PWWP1

Canonical annotation interval 11–68 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.

Alternative PWWP annotations and interval provenance
[
  {
    "end": 96,
    "identifier": "cd20150",
    "integrated_identifier": null,
    "model": "cd20150",
    "name": "PWWP domain found in Hepatoma-derived growth factor-related protein 3 (HDGFL3)",
    "representative": false,
    "score": 1.99805e-61,
    "source": "cdd",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9Y3E1/?page_size=200",
    "start": 4
  },
  {
    "end": 66,
    "identifier": "SM00293",
    "integrated_identifier": "IPR000313",
    "model": "SM00293",
    "name": "domain with conserved PWWP motif",
    "representative": false,
    "score": 4.3e-19,
    "source": "smart",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9Y3E1/?page_size=200",
    "start": 9
  },
  {
    "end": 91,
    "identifier": "IPR000313",
    "integrated_identifier": null,
    "model": null,
    "name": "PWWP domain",
    "representative": false,
    "score": null,
    "source": "interpro",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9Y3E1/?page_size=200",
    "start": 9
  },
  {
    "end": 68,
    "identifier": "PS50812",
    "integrated_identifier": "IPR000313",
    "model": "PS50812",
    "name": "PWWP domain profile",
    "representative": false,
    "score": null,
    "source": "profile",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9Y3E1/?page_size=200",
    "start": 11
  },
  {
    "end": 91,
    "identifier": "PF00855",
    "integrated_identifier": "IPR000313",
    "model": "PF00855",
    "name": "PWWP domain",
    "representative": false,
    "score": 2.2e-14,
    "source": "pfam",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9Y3E1/?page_size=200",
    "start": 12
  }
]

PWWP1 · source-classified Phase 6A evidence

Ligands & Bioactivity

Explore all domain compounds →

1 chemical or preparation profiles · 1 domain-attributed assay / association observations. Counts refer to the curated snapshot.

0 profiles

Deposited research ligands

No records in this category for the selected domain in the curated snapshot.

0 profiles

Experiment-specific controls

No records in this category for the selected domain in the curated snapshot.

0 profiles

Ambiguous / indirect evidence

No records in this category for the selected domain in the curated snapshot.

4 other deposited components in this domain (not pharmacological ligands)

Buffers, ions, cryoprotectants and solvents remain recorded as deposited chemical components.

2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL · Other PDB component · not a studied ligandMALONIC ACID · Other PDB component · not a studied ligandSULFATE ION · Other PDB component · not a studied ligand2-(N-MORPHOLINO)-ETHANESULFONIC ACID · Other PDB component · not a studied ligand

Open this domain in Structural & Binding Landscape →

PWWP1 · Deposited coordinates

Experimental coverage and AlphaFold correspondence

5 entry / domain records

One representative chain per PDB entry and native domain. RMSD uses fixed UniProt correspondence and all common Cα atoms; it is reported only for ≥40 atoms and ≥80% core coverage. A value is descriptive, not a prediction benchmark.

PDBChainObserved core CαClassMethod / resolutionAF RMSD ÅReview
6IIPA58 / 58APOX-RAY DIFFRACTION
0.951 Å		1.31No classification flag
6IIQA58 / 58ComplexesX-RAY DIFFRACTION
1.85 Å		0.509No classification flag
6IIRA58 / 58ComplexesX-RAY DIFFRACTION
2.2 Å		0.534No classification flag
6IISA58 / 58ComplexesX-RAY DIFFRACTION
2.358 Å		0.493No classification flag
6IITA58 / 58ComplexesX-RAY DIFFRACTION
2.1 Å		0.51No classification flag

PWWP1 · Measured preparations

Frozen v1.2 assay records

Explore evidence links

This retained table is the original source projection. The Phase 5 Ligands & Bioactivity section above includes added observations and reviewed target context. Values remain attached to their assay, construct and preparation. A crystal structure does not transfer affinity to another construct or stereoisomer. Assay pages preserve field-level source-verification states where reviewed; unreviewed null fields remain uncurated.

Preparation / identityAssay and resultConstructEvidence and source
BPP
exact single CCD identity		Binding Kd; specific assay in Figure S2 not independently inspected
= 14.0 µM ± 2.0
direct binding affinity		UncuratedPMID:39031937
primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved

14 ± 2 µM confirmed in primary Results; specific Figure S2 assay method remains unresolved.

Assay conditions and interpretation

{}

Numerical result verified in main text; precise supporting-assay details remain to be checked.

Scientific review queue

PWWP1 · Prediction evidence

Predicted models

1 model records

Domain retention uses independently reconstructed UniProt isoform edits. Local pLDDT is not experimental confirmation and does not establish interdomain orientation.

ModelOriginCore retentionCore mean pLDDTFull mean pLDDTCautions
AF-Q9Y3E1-F1:v6
Canonical		GDMcomplete89.170.7

PWWP1 · Structural correspondence

Human annotation-core comparisons

17 pairs

Structural alignment establishes a residue correspondence for these cropped cores. It does not establish equivalent ligand pockets, function or selectivity.

Domain pairAligned CαUS-align RMSD ÅTM score A / BView
ARID4A PWWP1 HDGFL3 PWWP1571.970.51 / 0.745Aligned core viewer
BRD1 PWWP1 HDGFL3 PWWP1582.880.549 / 0.754Aligned core viewer
BRPF1 PWWP1 HDGFL3 PWWP1582.180.578 / 0.794Aligned core viewer
BRPF3 PWWP1 HDGFL3 PWWP1582.190.57 / 0.781Aligned core viewer
DNMT3A PWWP1 HDGFL3 PWWP1581.720.849 / 0.862Aligned core viewer
DNMT3B PWWP1 HDGFL3 PWWP1581.710.848 / 0.861Aligned core viewer
HDGF PWWP1 HDGFL3 PWWP1572.090.738 / 0.738Aligned core viewer
HDGFL2 PWWP1 HDGFL3 PWWP1571.040.923 / 0.923Aligned core viewer
HDGFL3 PWWP1 MSH6 PWWP1561.960.769 / 0.72Aligned core viewer
HDGFL3 PWWP1 NSD2 PWWP1551.80.783 / 0.71Aligned core viewer
HDGFL3 PWWP1 NSD3 PWWP1561.960.774 / 0.713Aligned core viewer
HDGFL3 PWWP1 NSD3 PWWP2582.490.732 / 0.685Aligned core viewer
HDGFL3 PWWP1 PSIP1 PWWP1571.530.788 / 0.73Aligned core viewer
HDGFL3 PWWP1 PWWP2B PWWP1521.940.765 / 0.731Aligned core viewer
HDGFL3 PWWP1 PWWP3A PWWP1502.180.676 / 0.64Aligned core viewer
HDGFL3 PWWP1 ZMYND11 PWWP1512.120.689 / 0.749Aligned core viewer
HDGFL3 PWWP1 ZMYND8 PWWP1512.060.69 / 0.762Aligned core viewer