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

Native domain record

NSD2 PWWP2

Histone-lysine N-methyltransferase NSD2

O96028 at UniProt
Homo sapiens1365 amino acidsannotation supportedUP:O96028:PWWP2
2annotated cores in NSD2
0PDB entries with observed PWWP2 coordinates
7model records for PWWP2
0frozen v1.2 assay / association records for PWWP2

Canonical sequence · Source-mapped regions

Protein domain architecture

1365 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 · 222–286 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket PWWP2 · 880–942 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket Other source annotations Zinc finger: PHD-type 1 · 667–713 · UniProtKB source annotation Zinc finger: PHD-type 2 · 714–770 · UniProtKB source annotation Zinc finger: PHD-type 3 · 831–875 · UniProtKB source annotation Domain: AWS · 1011–1061 · UniProtKB source annotation Domain: SET · 1063–1180 · UniProtKB source annotation Domain: Post-SET · 1187–1203 · UniProtKB source annotation Zinc finger: PHD-type 4; atypical · 1239–1286 · UniProtKB source annotation 1 341 682 1024 1365
PWWP annotation coreOther source annotationPredicted candidate, when present
7 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
PHD-type 1Zinc finger667–713ECO:0000255 PROSITE-ProRule: PRU00146
PHD-type 2Zinc finger714–770ECO:0000255 PROSITE-ProRule: PRU00146
PHD-type 3Zinc finger831–875ECO:0000255 PROSITE-ProRule: PRU00146
AWSDomain1011–1061ECO:0000255 PROSITE-ProRule: PRU00562
SETDomain1063–1180ECO:0000255 PROSITE-ProRule: PRU00190
Post-SETDomain1187–1203ECO:0000255 PROSITE-ProRule: PRU00155
PHD-type 4; atypicalZinc finger1239–1286ECO:0000255 PROSITE-ProRule: PRU00146

Deposited construct mapping

4 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.

9FOCchain A208–368
Mapped deposited segment 208–368 Observed canonical residues 215–295Observed canonical residues 315–365
Mapping and construct evidence

Deposited polymer length: 176 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 65 / 65 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: 1–4, 166–176.

5VC8chain B211–350
Mapped deposited segment 211–350 Observed canonical residues 217–301Observed canonical residues 310–350
Mapping and construct evidence

Deposited polymer length: 141 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 65 / 65 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.

9Y60chain A202–368
Mapped deposited segment 202–368 Observed canonical residues 203–368
Mapping and construct evidence

Deposited polymer length: 174 residues. Mapped sequence identity: 99.4%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 65 / 65 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": "A",
    "entity_position": 161,
    "reference": "K",
    "uniprot_position": 361
  }
]

Unmapped construct positions: 1–1, 169–174.

29HGchain B1–1365
Mapped deposited segment 1–1365 Observed canonical residues 212–300Observed canonical residues 316–362
Mapping and construct evidence

Deposited polymer length: 1365 residues. Mapped sequence identity: 100.0%. no sequence difference detected by mapping; not proof of wild type.

PWWP1: 65 / 65 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 · 12 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
O96028-2713PWWP1Noneabsent

Official deletion removes entire annotated core; incidental alignment matches cannot restore deleted residues.

Official sequence edits

VSP_021414 · canonical 1–652 · deletion

VSP_021423 · canonical 653–712 · equal length replacement

O96028-2713PWWP2228–290
63 / 63 mapped residues; span may contain gaps		complete
O96028-3647PWWP1222–286
65 / 65 mapped residues; span may contain gaps		complete
O96028-3647PWWP2Noneabsent

Official deletion removes entire annotated core; incidental alignment matches cannot restore deleted residues.

Official sequence edits

VSP_021419 · canonical 628–647 · equal length replacement

VSP_021422 · canonical 648–1365 · deletion

O96028-4584PWWP1Noneabsent
O96028-4584PWWP299–161
63 / 63 mapped residues; span may contain gaps		complete
O96028-5629PWWP1222–286
65 / 65 mapped residues; span may contain gaps		complete
O96028-5629PWWP2Noneabsent
O96028-6484PWWP1222–286
65 / 65 mapped residues; span may contain gaps		complete
O96028-6484PWWP2Noneabsent
O96028-7273PWWP1222–273
52 / 65 mapped residues; span may contain gaps		partial

Use source-defined positions for equal-length replacement; replacement is not unchanged sequence.

Official sequence edits

VSP_021415 · canonical 255–273 · equal length replacement

VSP_021416 · canonical 274–1365 · deletion

O96028-7273PWWP2Noneabsent
Viewing NSD2 PWWP2

Canonical annotation interval 880–942 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.

Alternative PWWP annotations and interval provenance
[
  {
    "end": 940,
    "identifier": "SM00293",
    "integrated_identifier": "IPR000313",
    "model": "SM00293",
    "name": "domain with conserved PWWP motif",
    "representative": false,
    "score": 4.6e-23,
    "source": "smart",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/O96028/?page_size=200",
    "start": 878
  },
  {
    "end": 969,
    "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/O96028/?page_size=200",
    "start": 878
  },
  {
    "end": 974,
    "identifier": "IPR047435",
    "integrated_identifier": null,
    "model": null,
    "name": "Nuclear SET domain-containing protein 2, second PWWP domain",
    "representative": false,
    "score": null,
    "source": "interpro",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/O96028/?page_size=200",
    "start": 879
  },
  {
    "end": 974,
    "identifier": "cd20165",
    "integrated_identifier": "IPR047435",
    "model": "cd20165",
    "name": "second PWWP domain found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins",
    "representative": false,
    "score": 4.17223e-72,
    "source": "cdd",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/O96028/?page_size=200",
    "start": 879
  },
  {
    "end": 942,
    "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/O96028/?page_size=200",
    "start": 880
  },
  {
    "end": 969,
    "identifier": "PF00855",
    "integrated_identifier": "IPR000313",
    "model": "PF00855",
    "name": "PWWP domain",
    "representative": false,
    "score": 8.5e-20,
    "source": "pfam",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/O96028/?page_size=200",
    "start": 882
  }
]

PWWP2 · source-classified Phase 6A evidence

Ligands & Bioactivity

Explore all domain compounds →

0 chemical or preparation profiles · 0 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.

0 profiles

Ambiguous / indirect evidence

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

14 protein-level observations — no specific PWWP-domain attribution

These observations concern NSD2 in its reported experimental context. They are excluded from the selected domain's measurement counts.

Open this domain in Structural & Binding Landscape →

Phase 6B · newly investigated source evidence

Additional experimental observations

Explore Phase 6B evidence

No newly accepted exact-domain observations for this specific PWWP instance.

2 new whole-protein cellular degradation results — NOT assigned to PWWP2

No new unmodified parent binary PWWP-bound PDB structure is claimed for these entries. Original Phase 5/6A numbers remain unchanged.

PWWP2 · Deposited coordinates

Experimental coverage and AlphaFold correspondence

4 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
29HGB0 / 63ComplexesELECTRON MICROSCOPY
4.0 Å		—No classification flag
29HHB0 / 63ComplexesELECTRON MICROSCOPY
4.2 Å		—No classification flag
29HIB0 / 63ComplexesELECTRON MICROSCOPY
5.9 Å		—No classification flag
7CROK0 / 63Unclassified_ReviewELECTRON MICROSCOPY
3.75 Å		—Required

PWWP2 · 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
No curated assay row for this domain. This does not establish that no literature evidence exists.

Scientific review queue

PWWP2 · Prediction evidence

Predicted models

7 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-O96028-F1:v6
Canonical		GDMcomplete89.865.6
AF-O96028-2-F1:v6GDMcomplete9379.1
AF-O96028-3-F1:v6GDMabsent—59.3partial_or_absent_mapped_core
AF-O96028-4-F1:v6GDMcomplete92.983.2
AF-O96028-5-F1:v6GDMabsent—59.1partial_or_absent_mapped_core
AF-O96028-6-F1:v6GDMabsent—61.6partial_or_absent_mapped_core
AF-O96028-7-F1:v6GDMabsent—55.4partial_or_absent_mapped_core

PWWP2 · Structural correspondence

Human annotation-core comparisons

0 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
No eligible experimental representative for a cross-domain comparison.