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

Native domain record

NSD3 PWWP2

Histone-lysine N-methyltransferase NSD3

Q9BZ95 at UniProt
Homo sapiens1437 amino acidsannotation supportedUP:Q9BZ95:PWWP2
2annotated cores in NSD3
2PDB entries with observed PWWP2 coordinates
5model records for PWWP2
0frozen v1.2 assay / association records for PWWP2

Canonical sequence · Source-mapped regions

Protein domain architecture

1437 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 · 270–333 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket PWWP2 · 960–1022 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket Other source annotations Zinc finger: PHD-type 1 · 701–748 · UniProtKB source annotation Zinc finger: PHD-type 2 · 749–805 · UniProtKB source annotation Zinc finger: PHD-type 3 · 862–955 · UniProtKB source annotation Domain: AWS · 1093–1143 · UniProtKB source annotation Domain: SET · 1145–1262 · UniProtKB source annotation Domain: Post-SET · 1269–1285 · UniProtKB source annotation Zinc finger: PHD-type 4; atypical · 1321–1368 · UniProtKB source annotation 1 359 718 1078 1437
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 finger701–748ECO:0000255 PROSITE-ProRule: PRU00146
PHD-type 2Zinc finger749–805ECO:0000255 PROSITE-ProRule: PRU00146
PHD-type 3Zinc finger862–955ECO:0000255 PROSITE-ProRule: PRU00146
AWSDomain1093–1143ECO:0000255 PROSITE-ProRule: PRU00562
SETDomain1145–1262ECO:0000255 PROSITE-ProRule: PRU00190
Post-SETDomain1269–1285ECO:0000255 PROSITE-ProRule: PRU00155
PHD-type 4; atypicalZinc finger1321–1368ECO: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.

6G25chain A263–398
Mapped deposited segment 263–398 Observed canonical residues 266–343Observed canonical residues 354–396
Mapping and construct evidence

Deposited polymer length: 136 residues. Mapped sequence identity: 100.0%. no sequence difference detected by mapping; not proof of wild type.

PWWP1: 64 / 64 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.

4RXJchain A953–1064
Mapped deposited segment 953–1064 Observed canonical residues 957–1064
Mapping and construct evidence

Deposited polymer length: 113 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP2: 63 / 63 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.

2DAQchain A957–1053
Mapped deposited segment 957–1053 Observed canonical residues 957–1053
Mapping and construct evidence

Deposited polymer length: 110 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP2: 63 / 63 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: 1–7, 105–110.

6G3Pchain A247–398
Mapped deposited segment 247–398 Observed canonical residues 249–256Observed canonical residues 264–343Observed canonical residues 360–395
Mapping and construct evidence

Deposited polymer length: 153 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 64 / 64 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 · 8 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
Q9BZ95-21388PWWP1270–333
64 / 64 mapped residues; span may contain gaps		complete
Q9BZ95-21388PWWP2911–973
63 / 63 mapped residues; span may contain gaps		complete
Q9BZ95-3645PWWP1270–333
64 / 64 mapped residues; span may contain gaps		complete
Q9BZ95-3645PWWP2Noneabsent
Q9BZ95-41374PWWP1207–270
64 / 64 mapped residues; span may contain gaps		complete
Q9BZ95-41374PWWP2897–959
63 / 63 mapped residues; span may contain gaps		complete
Q9BZ95-51426PWWP1270–333
64 / 64 mapped residues; span may contain gaps		complete
Q9BZ95-51426PWWP2960–1022
63 / 63 mapped residues; span may contain gaps		complete
Viewing NSD3 PWWP2

Canonical annotation interval 960–1022 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.

Alternative PWWP annotations and interval provenance
[
  {
    "end": 1020,
    "identifier": "SM00293",
    "integrated_identifier": "IPR000313",
    "model": "SM00293",
    "name": "domain with conserved PWWP motif",
    "representative": false,
    "score": 2.2e-17,
    "source": "smart",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 958
  },
  {
    "end": 1048,
    "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/Q9BZ95/?page_size=200",
    "start": 958
  },
  {
    "end": 1053,
    "identifier": "IPR047453",
    "integrated_identifier": null,
    "model": null,
    "name": "Histone-lysine N-methyltransferase NSD3, second PWWP domain",
    "representative": false,
    "score": null,
    "source": "interpro",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 959
  },
  {
    "end": 1053,
    "identifier": "cd20166",
    "integrated_identifier": "IPR047453",
    "model": "cd20166",
    "name": "second PWWP domain found in nuclear SET domain-containing protein 3 (NSD3) and similar proteins",
    "representative": false,
    "score": 7.50168e-72,
    "source": "cdd",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 959
  },
  {
    "end": 1022,
    "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/Q9BZ95/?page_size=200",
    "start": 960
  },
  {
    "end": 1048,
    "identifier": "PF00855",
    "integrated_identifier": "IPR000313",
    "model": "PF00855",
    "name": "PWWP domain",
    "representative": false,
    "score": 2.6e-19,
    "source": "pfam",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 962
  }
]

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.

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

These observations concern NSD3 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.

9 source-reported NSD3 PWWP results with an unresolved domain instance

PWWP1/PWWP2 attribution and the actual purified construct are not verified. These are excluded from exact-domain counts.

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

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
2DAQA63 / 63APOSOLUTION NMR1.67No classification flag
4RXJA63 / 63Unclassified_ReviewX-RAY DIFFRACTION
2.1 Å		1.39Required
7CRPK0 / 63Unclassified_ReviewELECTRON MICROSCOPY
3.2 Å		—Required
7CRQK0 / 63Unclassified_ReviewELECTRON MICROSCOPY
3.15 Å		—Required
7CRRK0 / 63Unclassified_ReviewELECTRON MICROSCOPY
3.48 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

5 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-Q9BZ95-F1:v6
Canonical		GDMcomplete87.161.9
AF-Q9BZ95-2-F1:v6GDMcomplete88.563.8
AF-Q9BZ95-3-F1:v6GDMabsent—54.6partial_or_absent_mapped_core
AF-Q9BZ95-4-F1:v6GDMcomplete86.463.6
AF-Q9BZ95-5-F1:v6GDMcomplete87.661.5

PWWP2 · 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 NSD3 PWWP2591.910.533 / 0.736Aligned core viewer
BRD1 PWWP1 NSD3 PWWP2632.450.6 / 0.76Aligned core viewer
BRPF1 PWWP1 NSD3 PWWP2632.10.631 / 0.805Aligned core viewer
BRPF3 PWWP1 NSD3 PWWP2631.950.638 / 0.817Aligned core viewer
DNMT3A PWWP1 NSD3 PWWP2582.450.755 / 0.716Aligned core viewer
DNMT3B PWWP1 NSD3 PWWP2592.420.765 / 0.726Aligned core viewer
HDGF PWWP1 NSD3 PWWP2562.750.665 / 0.626Aligned core viewer
HDGFL2 PWWP1 NSD3 PWWP2572.180.769 / 0.719Aligned core viewer
HDGFL3 PWWP1 NSD3 PWWP2582.490.732 / 0.685Aligned core viewer
MSH6 PWWP1 NSD3 PWWP2562.40.666 / 0.666Aligned core viewer
NSD2 PWWP1 NSD3 PWWP2542.280.654 / 0.671Aligned core viewer
NSD3 PWWP1 NSD3 PWWP2552.40.661 / 0.669Aligned core viewer
NSD3 PWWP2 PSIP1 PWWP1572.650.666 / 0.658Aligned core viewer
NSD3 PWWP2 PWWP2B PWWP1502.480.632 / 0.649Aligned core viewer
NSD3 PWWP2 PWWP3A PWWP1502.420.583 / 0.59Aligned core viewer
NSD3 PWWP2 ZMYND11 PWWP1502.810.596 / 0.694Aligned core viewer
NSD3 PWWP2 ZMYND8 PWWP1512.570.619 / 0.735Aligned core viewer