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

Protein record

DNMT3B

DNA (cytosine-5)-methyltransferase 3B

Q9UBC3 at UniProt
Homo sapiens853 amino acidsannotation supported
1annotated core in DNMT3B
14PDB entries with observed PWWP1 coordinates
8model records for PWWP1
1frozen v1.2 assay / association records for PWWP1

Canonical sequence · Source-mapped regions

Protein domain architecture

853 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 · 225–283 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket Other source annotations Domain: ADD · 423–555 · UniProtKB source annotation Zinc finger: GATA-type; atypical · 434–464 · UniProtKB source annotation Zinc finger: PHD-type; atypical · 475–531 · UniProtKB source annotation Domain: SAM-dependent MTase C5-type · 575–853 · UniProtKB source annotation 1 213 426 640 853
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
ADDDomain423–555ECO:0000255 PROSITE-ProRule: PRU00865
GATA-type; atypicalZinc finger434–464ECO:0000255 PROSITE-ProRule: PRU00865
PHD-type; atypicalZinc finger475–531ECO:0000255 PROSITE-ProRule: PRU00865
SAM-dependent MTase C5-typeDomain575–853ECO: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.

5NRRchain A206–355
Mapped deposited segment 206–355 Observed canonical residues 213–319Observed canonical residues 324–351
Mapping and construct evidence

Deposited polymer length: 150 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.

6R3Echain A215–351
Mapped deposited segment 215–351 Observed canonical residues 215–319Observed canonical residues 324–351
Mapping and construct evidence

Deposited polymer length: 274 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.

8EIHchain E206–853
Mapped deposited segment 206–853 Observed canonical residues 216–313Observed canonical residues 327–350
Mapping and construct evidence

Deposited polymer length: 650 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: 1–2.

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

Validated isoform differences · 7 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
Q9UBC3-2833PWWP1225–283
59 / 59 mapped residues; span may contain gaps		complete
Q9UBC3-3770PWWP1225–283
59 / 59 mapped residues; span may contain gaps		complete
Q9UBC3-4724PWWP1225–283
59 / 59 mapped residues; span may contain gaps		complete
Q9UBC3-5792PWWP1225–283
59 / 59 mapped residues; span may contain gaps		complete
Q9UBC3-6845PWWP1237–295
59 / 59 mapped residues; span may contain gaps		complete
Q9UBC3-7694PWWP1149–207
59 / 59 mapped residues; span may contain gaps		complete
Q9UBC3-8728PWWP1183–241
59 / 59 mapped residues; span may contain gaps		complete
Viewing DNMT3B PWWP1

Canonical annotation interval 225–283 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.

Alternative PWWP annotations and interval provenance
[
  {
    "end": 281,
    "identifier": "SM00293",
    "integrated_identifier": "IPR000313",
    "model": "SM00293",
    "name": "domain with conserved PWWP motif",
    "representative": false,
    "score": 2.3e-26,
    "source": "smart",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9UBC3/?page_size=200",
    "start": 223
  },
  {
    "end": 309,
    "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/Q9UBC3/?page_size=200",
    "start": 223
  },
  {
    "end": 340,
    "identifier": "cd20155",
    "integrated_identifier": null,
    "model": "cd20155",
    "name": "PWWP domain found in DNA (cytosine-5)-methyltransferase 3B (DNMT3B)",
    "representative": false,
    "score": 1.8189e-83,
    "source": "cdd",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9UBC3/?page_size=200",
    "start": 224
  },
  {
    "end": 283,
    "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/Q9UBC3/?page_size=200",
    "start": 225
  },
  {
    "end": 309,
    "identifier": "PF00855",
    "integrated_identifier": "IPR000313",
    "model": "PF00855",
    "name": "PWWP domain",
    "representative": false,
    "score": 1.5e-10,
    "source": "pfam",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9UBC3/?page_size=200",
    "start": 226
  }
]

PWWP1 · source-classified Phase 6A evidence

Ligands & Bioactivity

Explore all domain compounds →

11 chemical or preparation profiles · 2 domain-attributed assay / association observations. Counts refer to the curated snapshot.

9 profiles

Deposited research ligands

(2~{S})-1-[2-hydroxyethyl-[(2~{S})-2-oxidanylpropyl]amino]propan-2-ol0 observations · 1 research-ligand entries(2~{S})-6-methyl-~{N}-propan-2-yl-heptan-2-amine0 observations · 1 research-ligand entries4-(dipropylamino)butanenitrile0 observations · 1 research-ligand entries5-[2-hydroxyethyl(propyl)amino]pentan-1-ol0 observations · 1 research-ligand entries6-dipropylamino-1-hexanol0 observations · 1 research-ligand entriesCHOLINE ION0 observations · 1 research-ligand entriesEthambutol0 observations · 1 research-ligand entriesN1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine0 observations · 1 research-ligand entriesTriisopropanolamine0 observations · 1 research-ligand entries

0 profiles

Experiment-specific controls

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

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

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

GLYCEROL · Other PDB component · not a studied ligandSULFATE ION · Other PDB component · not a studied ligand

Open this domain in Structural & Binding Landscape →

PWWP1 · Deposited coordinates

Experimental coverage and AlphaFold correspondence

30 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
3FLGA59 / 59APOX-RAY DIFFRACTION
1.8 Å		0.843No classification flag
3QKJA59 / 59APOX-RAY DIFFRACTION
2.04 Å		0.353No classification flag
5CIUA59 / 59ComplexesX-RAY DIFFRACTION
2.24 Å		0.456No classification flag
5NR3A59 / 59Co-CrystalsX-RAY DIFFRACTION
2.3 Å		0.313No classification flag
5NRRA59 / 59Co-CrystalsX-RAY DIFFRACTION
1.7 Å		0.389No classification flag
5NRSA59 / 59Co-CrystalsX-RAY DIFFRACTION
2.3 Å		0.304No classification flag
5NRVA59 / 59Co-CrystalsX-RAY DIFFRACTION
2.075 Å		0.446No classification flag
5NV0A59 / 59Co-CrystalsX-RAY DIFFRACTION
2.399 Å		0.436No classification flag
5NV2A59 / 59Co-CrystalsX-RAY DIFFRACTION
2.029 Å		0.29No classification flag
5NV7A59 / 59Co-CrystalsX-RAY DIFFRACTION
2.568 Å		0.329No classification flag
5NVOA59 / 59Co-CrystalsX-RAY DIFFRACTION
2.4 Å		0.332No classification flag
6R3EA59 / 59Co-CrystalsX-RAY DIFFRACTION
2.269 Å		0.338No classification flag
8EIHE59 / 59ComplexesELECTRON MICROSCOPY
3.04 Å		1.28No classification flag
8ZLKA59 / 59APOX-RAY DIFFRACTION
2.74 Å		0.375No classification flag
6PA7L0 / 59Unclassified_ReviewELECTRON MICROSCOPY
2.94 Å		—Required
8EIIA0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.12 Å		—Required
8EIJA0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.34 Å		—Required
8EIKA0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.19 Å		—Required
9E00S0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.75 Å		—Required
9E05S0 / 59ComplexesELECTRON MICROSCOPY
8.0 Å		—No classification flag
9E0FA0 / 59ComplexesELECTRON MICROSCOPY
3.46 Å		—No classification flag
9E0GA0 / 59ComplexesELECTRON MICROSCOPY
3.72 Å		—No classification flag
9E2DQ0 / 59ComplexesELECTRON MICROSCOPY
6.08 Å		—No classification flag
9E2QS0 / 59Unclassified_ReviewELECTRON MICROSCOPY
3.14 Å		—Required
9E2RS0 / 59ComplexesELECTRON MICROSCOPY
7.71 Å		—No classification flag
9E3DS0 / 59ComplexesELECTRON MICROSCOPY
3.8 Å		—No classification flag
9E3RS0 / 59Unclassified_ReviewELECTRON MICROSCOPY
6.9 Å		—Required
9E3UI0 / 59Unclassified_ReviewELECTRON MICROSCOPY
4.9 Å		—Required
9Q7UK0 / 59ComplexesELECTRON MICROSCOPY
3.4 Å		—No classification flag
9Y4PS0 / 59ComplexesELECTRON MICROSCOPY
3.84 Å		—No 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
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

8 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-Q9UBC3-F1:v6
Canonical		GDMcomplete89.872.5
AF-Q9UBC3-2-F1:v6GDMcomplete87.972.9
AF-Q9UBC3-3-F1:v6GDMcomplete9067.9
AF-Q9UBC3-4-F1:v6GDMcomplete8969.5
AF-Q9UBC3-5-F1:v6GDMcomplete89.167.8
AF-Q9UBC3-6-F1:v6GDMcomplete87.972.2
AF-Q9UBC3-7-F1:v6GDMcomplete87.171.9
AF-Q9UBC3-8-F1:v6GDMcomplete89.769.9

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 DNMT3B PWWP1591.720.544 / 0.795Aligned core viewer
BRD1 PWWP1 DNMT3B PWWP1592.520.569 / 0.766Aligned core viewer
BRPF1 PWWP1 DNMT3B PWWP1591.90.596 / 0.807Aligned core viewer
BRPF3 PWWP1 DNMT3B PWWP1591.870.595 / 0.803Aligned core viewer
DNMT3A PWWP1 DNMT3B PWWP1590.370.981 / 0.981Aligned core viewer
DNMT3B PWWP1 HDGF PWWP1551.970.693 / 0.701Aligned core viewer
DNMT3B PWWP1 HDGFL2 PWWP1581.190.863 / 0.876Aligned core viewer
DNMT3B PWWP1 HDGFL3 PWWP1581.710.848 / 0.861Aligned core viewer
DNMT3B PWWP1 MSH6 PWWP1561.760.802 / 0.758Aligned core viewer
DNMT3B PWWP1 NSD2 PWWP1551.50.792 / 0.728Aligned core viewer
DNMT3B PWWP1 NSD3 PWWP1561.680.784 / 0.732Aligned core viewer
DNMT3B PWWP1 NSD3 PWWP2592.420.765 / 0.726Aligned core viewer
DNMT3B PWWP1 PSIP1 PWWP1571.980.775 / 0.726Aligned core viewer
DNMT3B PWWP1 PWWP2B PWWP1521.830.761 / 0.738Aligned core viewer
DNMT3B PWWP1 PWWP3A PWWP1512.00.699 / 0.671Aligned core viewer
DNMT3B PWWP1 ZMYND11 PWWP1511.890.705 / 0.781Aligned core viewer
DNMT3B PWWP1 ZMYND8 PWWP1511.790.715 / 0.807Aligned core viewer