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

Protein record

DNMT3A

DNA (cytosine-5)-methyltransferase 3A

Q9Y6K1 at UniProt
Homo sapiens912 amino acidsannotation supported
1annotated core in DNMT3A
14PDB entries with observed PWWP1 coordinates
3model records for PWWP1
1frozen v1.2 assay / association records for PWWP1

Canonical sequence · Source-mapped regions

Protein domain architecture

912 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 · 292–350 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket Other source annotations Domain: ADD · 482–614 · UniProtKB source annotation Zinc finger: GATA-type; atypical · 493–523 · UniProtKB source annotation Zinc finger: PHD-type; atypical · 534–590 · UniProtKB source annotation Domain: SAM-dependent MTase C5-type · 634–912 · UniProtKB source annotation 1 228 456 684 912
PWWP annotation coreOther source annotationPredicted candidate, when present
4 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.

Source featureTypeAmino acidsEvidence
ADDDomain482–614ECO:0000255 PROSITE-ProRule: PRU00865
GATA-type; atypicalZinc finger493–523ECO:0000255 PROSITE-ProRule: PRU00865
PHD-type; atypicalZinc finger534–590ECO:0000255 PROSITE-ProRule: PRU00865
SAM-dependent MTase C5-typeDomain634–912ECO:0000255 PROSITE-ProRule: PRU01016

Deposited construct mapping

3 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.

3LLRchain A275–427
Mapped deposited segment 275–427 Observed canonical residues 283–385Observed canonical residues 398–425
Mapping and construct evidence

Deposited polymer length: 154 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 59 / 59 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.

11NZchain B281–912
Mapped deposited segment 281–912 Observed canonical residues 289–383Observed canonical residues 395–424Observed canonical residues 469–912
Mapping and construct evidence

Deposited polymer length: 633 residues. Mapped sequence identity: 99.84%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 59 / 59 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.

Source-recorded sequence differences:

[
  {
    "construct": "H",
    "entity_position": 603,
    "reference": "R",
    "uniprot_position": 882
  }
]

Unmapped construct positions: 1–1.

9E05chain V224–912
Mapped deposited segment 224–912 Observed canonical residues 283–385Observed canonical residues 398–425Observed canonical residues 476–832Observed canonical residues 846–912
Mapping and construct evidence

Deposited polymer length: 689 residues. Mapped sequence identity: 100.0%. no sequence difference detected by mapping; not proof of wild type.

PWWP1: 59 / 59 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.

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

Validated isoform differences · 2 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.

IsoformLengthPWWP coreSource-mapped positionsRetention / source edits
Q9Y6K1-2723PWWP1103–161
59 / 59 mapped residues; span may contain gaps		complete
Q9Y6K1-3166PWWP1Noneabsent
Viewing DNMT3A PWWP1

Canonical annotation interval 292–350 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.

Alternative PWWP annotations and interval provenance
[
  {
    "end": 418,
    "identifier": "cd20154",
    "integrated_identifier": null,
    "model": "cd20154",
    "name": "PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A)",
    "representative": false,
    "score": 1.4838e-102,
    "source": "cdd",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9Y6K1/?page_size=200",
    "start": 285
  },
  {
    "end": 348,
    "identifier": "SM00293",
    "integrated_identifier": "IPR000313",
    "model": "SM00293",
    "name": "domain with conserved PWWP motif",
    "representative": false,
    "score": 2.3e-24,
    "source": "smart",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9Y6K1/?page_size=200",
    "start": 290
  },
  {
    "end": 374,
    "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/Q9Y6K1/?page_size=200",
    "start": 290
  },
  {
    "end": 350,
    "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/Q9Y6K1/?page_size=200",
    "start": 292
  },
  {
    "end": 374,
    "identifier": "PF00855",
    "integrated_identifier": "IPR000313",
    "model": "PF00855",
    "name": "PWWP domain",
    "representative": false,
    "score": 1.6e-10,
    "source": "pfam",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9Y6K1/?page_size=200",
    "start": 293
  }
]

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

Studied without research structure

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.

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

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

SULFATE ION · Other PDB component · not a studied ligand

Open this domain in Structural & Binding Landscape →

PWWP1 · Deposited coordinates

Experimental coverage and AlphaFold correspondence

24 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
11NZB59 / 59ComplexesELECTRON MICROSCOPY
4.19 Å		1.39No classification flag
11OAC59 / 59ComplexesELECTRON MICROSCOPY
5.04 Å		1.46No classification flag
11OHC59 / 59ComplexesELECTRON MICROSCOPY
3.58 Å		1.29No classification flag
11OIA59 / 59ComplexesELECTRON MICROSCOPY
3.66 Å		1.28No classification flag
3LLRA59 / 59APOX-RAY DIFFRACTION
2.3 Å		0.429No classification flag
9E05V59 / 59ComplexesELECTRON MICROSCOPY
8.0 Å		0.717No classification flag
9E0FD59 / 59ComplexesELECTRON MICROSCOPY
3.46 Å		0.717No classification flag
9E0GD59 / 59ComplexesELECTRON MICROSCOPY
3.72 Å		0.681No classification flag
9E2DT59 / 59ComplexesELECTRON MICROSCOPY
6.08 Å		0.718No classification flag
9E2RV59 / 59ComplexesELECTRON MICROSCOPY
7.71 Å		0.718No classification flag
9E3DV59 / 59ComplexesELECTRON MICROSCOPY
3.8 Å		0.718No classification flag
9PRWD59 / 59ComplexesELECTRON MICROSCOPY
3.66 Å		1.24No classification flag
9Q7UM59 / 59ComplexesELECTRON MICROSCOPY
3.4 Å		0.819No classification flag
9Y4PU59 / 59ComplexesELECTRON MICROSCOPY
3.84 Å		0.994No classification flag
6PA7K0 / 59Unclassified_ReviewELECTRON MICROSCOPY
2.94 Å		—Required
8QZMK0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.1 Å		—Required
9E00U0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.75 Å		—Required
9E2QU0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.14 Å		—Required
9E3RU0 / 59Unclassified_ReviewELECTRON MICROSCOPY
6.9 Å		—Required
9E3UN0 / 59Unclassified_ReviewELECTRON MICROSCOPY
4.9 Å		—Required
9LQ1A0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.36 Å		—Required
9MP0A0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.66 Å		—Required
9MPOA0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.62 Å		—Required
9MPPK0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.1 Å		—Required

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
Bis-Tris
exact single CCD identity		No pharmacological activity assigned
No verified numeric value
structural occupancy association		UncuratedPMID:21720545
local_primary_full_text_XML; Tables 1-2, crystallization methods and ligand Results inspected

Pocket occupancy in high-concentration crystallization buffer is not evidence of potency.

Assay conditions and interpretation

{}

Observed aromatic-cage occupancy by crystallization buffer. Do not classify as a validated pharmacological ligand.

Scientific review queue

PWWP1 · Prediction evidence

Predicted models

3 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-Q9Y6K1-F1:v6
Canonical		GDMcomplete89.872.9
AF-Q9Y6K1-2-F1:v6GDMcomplete89.580.8
AF-Q9Y6K1-3-F1:v6GDMabsent—60.3partial_or_absent_mapped_core

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 DNMT3A PWWP1591.840.539 / 0.787Aligned core viewer
BRD1 PWWP1 DNMT3A PWWP1592.550.568 / 0.768Aligned core viewer
BRPF1 PWWP1 DNMT3A PWWP1581.80.598 / 0.811Aligned core viewer
BRPF3 PWWP1 DNMT3A PWWP1581.770.599 / 0.814Aligned core viewer
DNMT3A PWWP1 DNMT3B PWWP1590.370.981 / 0.981Aligned core viewer
DNMT3A PWWP1 HDGF PWWP1562.050.695 / 0.704Aligned core viewer
DNMT3A PWWP1 HDGFL2 PWWP1581.220.861 / 0.873Aligned core viewer
DNMT3A PWWP1 HDGFL3 PWWP1581.720.849 / 0.862Aligned core viewer
DNMT3A PWWP1 MSH6 PWWP1561.820.798 / 0.755Aligned core viewer
DNMT3A PWWP1 NSD2 PWWP1551.50.797 / 0.732Aligned core viewer
DNMT3A PWWP1 NSD3 PWWP1561.70.794 / 0.74Aligned core viewer
DNMT3A PWWP1 NSD3 PWWP2582.450.755 / 0.716Aligned core viewer
DNMT3A PWWP1 PSIP1 PWWP1561.70.775 / 0.726Aligned core viewer
DNMT3A PWWP1 PWWP2B PWWP1521.850.753 / 0.731Aligned core viewer
DNMT3A PWWP1 PWWP3A PWWP1522.320.691 / 0.664Aligned core viewer
DNMT3A PWWP1 ZMYND11 PWWP1511.810.725 / 0.807Aligned core viewer
DNMT3A PWWP1 ZMYND8 PWWP1511.820.723 / 0.817Aligned core viewer