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

Native domain record

ZMYND8 PWWP1

MYND-type zinc finger-containing chromatin reader ZMYND8

Q9ULU4 at UniProt
Homo sapiens1186 amino acidsannotation supportedUP:Q9ULU4:PWWP1
1annotated core in ZMYND8
5PDB entries with observed PWWP1 coordinates
23model records for PWWP1
0frozen v1.2 assay / association records for PWWP1

Canonical sequence · Source-mapped regions

Protein domain architecture

1186 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 · 277–327 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket Other source annotations Zinc finger: PHD-type · 88–133 · UniProtKB source annotation Domain: Bromo · 145–252 · UniProtKB source annotation Zinc finger: MYND-type · 1028–1062 · UniProtKB source annotation 1 296 593 890 1186
PWWP annotation coreOther source annotationPredicted candidate, when present
3 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-typeZinc finger88–133ECO:0000255 PROSITE-ProRule: PRU00146
BromoDomain145–252ECO:0000255 PROSITE-ProRule: PRU00035
MYND-typeZinc finger1028–1062ECO:0000255 PROSITE-ProRule: PRU00134

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.

9T2Gchain A83–406
Mapped deposited segment 83–406 Observed canonical residues 86–117Observed canonical residues 124–399
Mapping and construct evidence

Deposited polymer length: 326 residues. Mapped sequence identity: 99.38%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 51 / 51 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": "R",
    "entity_position": 121,
    "reference": "N",
    "uniprot_position": 201
  },
  {
    "construct": "H",
    "entity_position": 126,
    "reference": "M",
    "uniprot_position": 206
  }
]

Unmapped construct positions: 1–2.

5B73chain A73–406
Mapped deposited segment 73–406 Observed canonical residues 86–396Observed canonical residues 402–403
Mapping and construct evidence

Deposited polymer length: 339 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 51 / 51 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: 1–5.

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

Validated isoform differences · 22 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
Q9ULU4-101206PWWP1297–347
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-111214PWWP1277–327
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-121160PWWP1297–347
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-131188PWWP1297–347
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-141135PWWP1272–322
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-151088PWWP1272–322
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-161163PWWP1272–322
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-171054PWWP1272–322
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-181134PWWP1272–322
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-191241PWWP1304–354
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-2614PWWP1Noneabsent
Q9ULU4-201186PWWP1277–327
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-211115PWWP1252–302
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-221161PWWP1297–347
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-231105PWWP1214–264
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-3995PWWP1132–182
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-4764PWWP1Noneabsent
Q9ULU4-51181PWWP1272–322
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-61023PWWP1132–182
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-71234PWWP1297–347
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-81107PWWP1297–347
51 / 51 mapped residues; span may contain gaps		complete
Q9ULU4-91168PWWP1277–327
51 / 51 mapped residues; span may contain gaps		complete
Viewing ZMYND8 PWWP1

Canonical annotation interval 277–327 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.

Alternative PWWP annotations and interval provenance
[
  {
    "end": 362,
    "identifier": "cd20160",
    "integrated_identifier": null,
    "model": "cd20160",
    "name": "PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins",
    "representative": false,
    "score": 5.16607e-57,
    "source": "cdd",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9ULU4/?page_size=200",
    "start": 272
  },
  {
    "end": 325,
    "identifier": "SM00293",
    "integrated_identifier": "IPR000313",
    "model": "SM00293",
    "name": "domain with conserved PWWP motif",
    "representative": false,
    "score": 0.00016,
    "source": "smart",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9ULU4/?page_size=200",
    "start": 275
  },
  {
    "end": 348,
    "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/Q9ULU4/?page_size=200",
    "start": 275
  },
  {
    "end": 327,
    "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/Q9ULU4/?page_size=200",
    "start": 277
  },
  {
    "end": 348,
    "identifier": "PF00855",
    "integrated_identifier": "IPR000313",
    "model": "PF00855",
    "name": "PWWP domain",
    "representative": false,
    "score": 0.0029,
    "source": "pfam",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9ULU4/?page_size=200",
    "start": 280
  }
]

PWWP1 · 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 other deposited components in this domain (not pharmacological ligands)

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

1,2-ETHANEDIOL · Other PDB component · not a studied ligandSULFATE ION · Other PDB component · not a studied ligand1,4-DIETHYLENE DIOXIDE · 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
4COSA51 / 51APOX-RAY DIFFRACTION
1.67 Å		0.303No classification flag
5B73A51 / 51APOX-RAY DIFFRACTION
1.8 Å		0.316No classification flag
5Y1ZC51 / 51ComplexesX-RAY DIFFRACTION
2.676 Å		0.498No classification flag
9T2FA51 / 51APOX-RAY DIFFRACTION
1.68 Å		0.32No classification flag
9T2GA51 / 51APOX-RAY DIFFRACTION
1.66 Å		0.336No 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
No curated assay row for this domain. This does not establish that no literature evidence exists.

Scientific review queue

PWWP1 · Prediction evidence

Predicted models

23 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-Q9ULU4-F1:v6
Canonical		GDMcomplete95.558.4
AF-Q9ULU4-10-F1:v6GDMcomplete95.657.7
AF-Q9ULU4-11-F1:v6GDMcomplete95.657.9
AF-Q9ULU4-12-F1:v6GDMcomplete95.958.4
AF-Q9ULU4-13-F1:v6GDMcomplete95.958
AF-Q9ULU4-14-F1:v6GDMcomplete95.758.6
AF-Q9ULU4-15-F1:v6GDMcomplete95.859.9
AF-Q9ULU4-16-F1:v6GDMcomplete95.658.2
AF-Q9ULU4-17-F1:v6GDMcomplete95.760.6
AF-Q9ULU4-18-F1:v6GDMcomplete95.659.1
AF-Q9ULU4-19-F1:v6GDMcomplete95.457.3
AF-Q9ULU4-2-F1:v6GDMabsent—57partial_or_absent_mapped_core
AF-Q9ULU4-20-F1:v6GDMcomplete95.658
AF-Q9ULU4-21-F1:v6GDMcomplete95.559.6
AF-Q9ULU4-22-F1:v6GDMcomplete95.857.3
AF-Q9ULU4-23-F1:v6GDMcomplete95.556.2
AF-Q9ULU4-3-F1:v6GDMcomplete95.659.8
AF-Q9ULU4-4-F1:v6GDMabsent—53.9partial_or_absent_mapped_core
AF-Q9ULU4-5-F1:v6GDMcomplete95.958
AF-Q9ULU4-6-F1:v6GDMcomplete9659.1
AF-Q9ULU4-7-F1:v6GDMcomplete95.556.6
AF-Q9ULU4-8-F1:v6GDMcomplete95.759.2
AF-Q9ULU4-9-F1:v6GDMcomplete95.558.5

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 ZMYND8 PWWP1512.220.447 / 0.72Aligned core viewer
BRD1 PWWP1 ZMYND8 PWWP1492.220.49 / 0.747Aligned core viewer
BRPF1 PWWP1 ZMYND8 PWWP1512.250.507 / 0.773Aligned core viewer
BRPF3 PWWP1 ZMYND8 PWWP1512.190.512 / 0.786Aligned core viewer
DNMT3A PWWP1 ZMYND8 PWWP1511.820.723 / 0.817Aligned core viewer
DNMT3B PWWP1 ZMYND8 PWWP1511.790.715 / 0.807Aligned core viewer
HDGF PWWP1 ZMYND8 PWWP1502.220.625 / 0.683Aligned core viewer
HDGFL2 PWWP1 ZMYND8 PWWP1512.010.689 / 0.762Aligned core viewer
HDGFL3 PWWP1 ZMYND8 PWWP1512.060.69 / 0.762Aligned core viewer
MSH6 PWWP1 ZMYND8 PWWP1511.650.688 / 0.821Aligned core viewer
NSD2 PWWP1 ZMYND8 PWWP1501.310.674 / 0.825Aligned core viewer
NSD3 PWWP1 ZMYND8 PWWP1511.440.693 / 0.839Aligned core viewer
NSD3 PWWP2 ZMYND8 PWWP1512.570.619 / 0.735Aligned core viewer
PSIP1 PWWP1 ZMYND8 PWWP1511.980.636 / 0.758Aligned core viewer
PWWP2B PWWP1 ZMYND8 PWWP1511.830.698 / 0.81Aligned core viewer
PWWP3A PWWP1 ZMYND8 PWWP1502.190.61 / 0.705Aligned core viewer
ZMYND11 PWWP1 ZMYND8 PWWP1511.390.848 / 0.862Aligned core viewer