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

Protein record

MSH6

DNA mismatch repair protein Msh6

P52701 at UniProt
Homo sapiens1360 amino acidsannotation supported
1annotated core in MSH6
2PDB entries with observed PWWP1 coordinates
4model records for PWWP1
0frozen v1.2 assay / association records for PWWP1

Canonical sequence · Source-mapped regions

Protein domain architecture

1360 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 · 92–154 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket Other source annotations No additional eligible domain features in the retrieved source. 1 340 680 1020 1360
PWWP annotation coreOther source annotationPredicted candidate, when present
0 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.

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.

6OQMchain A87–198
Mapped deposited segment 87–198 Observed canonical residues 87–186
Mapping and construct evidence

Deposited polymer length: 130 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 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: 1–18.

2GFUchain A68–201
Mapped deposited segment 68–201 Observed canonical residues 68–201
Mapping and construct evidence

Deposited polymer length: 134 residues. Mapped sequence identity: 97.76%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 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.

Source-recorded sequence differences:

[
  {
    "construct": "S",
    "entity_position": 21,
    "reference": "C",
    "uniprot_position": 88
  },
  {
    "construct": "S",
    "entity_position": 41,
    "reference": "C",
    "uniprot_position": 108
  },
  {
    "construct": "S",
    "entity_position": 129,
    "reference": "C",
    "uniprot_position": 196
  }
]

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

Validated isoform differences · 3 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
P52701-21068PWWP192–154
63 / 63 mapped residues; span may contain gaps		complete
P52701-31230PWWP1Noneabsent
P52701-41058PWWP1Noneabsent
Viewing MSH6 PWWP1

Canonical annotation interval 92–154 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.

Alternative PWWP annotations and interval provenance
[
  {
    "end": 152,
    "identifier": "SM00293",
    "integrated_identifier": "IPR000313",
    "model": "SM00293",
    "name": "domain with conserved PWWP motif",
    "representative": false,
    "score": 2.4e-28,
    "source": "smart",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/P52701/?page_size=200",
    "start": 90
  },
  {
    "end": 183,
    "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/P52701/?page_size=200",
    "start": 90
  },
  {
    "end": 193,
    "identifier": "cd05837",
    "integrated_identifier": null,
    "model": "cd05837",
    "name": "PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins",
    "representative": false,
    "score": 3.53151e-56,
    "source": "cdd",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/P52701/?page_size=200",
    "start": 90
  },
  {
    "end": 154,
    "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/P52701/?page_size=200",
    "start": 92
  },
  {
    "end": 183,
    "identifier": "PF00855",
    "integrated_identifier": "IPR000313",
    "model": "PF00855",
    "name": "PWWP domain",
    "representative": false,
    "score": 3.7e-17,
    "source": "pfam",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/P52701/?page_size=200",
    "start": 93
  }
]

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.

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

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

MAGNESIUM ION · 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

3 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
2GFUA63 / 63APOSOLUTION NMR1.61No classification flag
6OQMA63 / 63Unclassified_ReviewX-RAY DIFFRACTION
2.2 Å		1.5Required
8AG6B0 / 63Unclassified_ReviewELECTRON MICROSCOPY
2.8 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
No curated assay row for this domain. This does not establish that no literature evidence exists.

Scientific review queue

PWWP1 · Prediction evidence

Predicted models

4 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-P52701-F1:v6
Canonical		GDMcomplete8277.1
AF-P52701-2-F1:v6GDMcomplete84.976.4
AF-P52701-3-F1:v6GDMabsent—77.5partial_or_absent_mapped_core
AF-P52701-4-F1:v6GDMabsent—83.6partial_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 MSH6 PWWP1572.520.488 / 0.668Aligned core viewer
BRD1 PWWP1 MSH6 PWWP1592.730.556 / 0.712Aligned core viewer
BRPF1 PWWP1 MSH6 PWWP1612.630.575 / 0.735Aligned core viewer
BRPF3 PWWP1 MSH6 PWWP1622.560.574 / 0.727Aligned core viewer
DNMT3A PWWP1 MSH6 PWWP1561.820.798 / 0.755Aligned core viewer
DNMT3B PWWP1 MSH6 PWWP1561.760.802 / 0.758Aligned core viewer
HDGF PWWP1 MSH6 PWWP1522.270.657 / 0.618Aligned core viewer
HDGFL2 PWWP1 MSH6 PWWP1562.130.761 / 0.713Aligned core viewer
HDGFL3 PWWP1 MSH6 PWWP1561.960.769 / 0.72Aligned core viewer
MSH6 PWWP1 NSD2 PWWP1621.420.838 / 0.816Aligned core viewer
MSH6 PWWP1 NSD3 PWWP1631.620.839 / 0.828Aligned core viewer
MSH6 PWWP1 NSD3 PWWP2562.40.666 / 0.666Aligned core viewer
MSH6 PWWP1 PSIP1 PWWP1562.50.659 / 0.652Aligned core viewer
MSH6 PWWP1 PWWP2B PWWP1562.10.708 / 0.727Aligned core viewer
MSH6 PWWP1 PWWP3A PWWP1532.330.629 / 0.637Aligned core viewer
MSH6 PWWP1 ZMYND11 PWWP1522.270.663 / 0.773Aligned core viewer
MSH6 PWWP1 ZMYND8 PWWP1511.650.688 / 0.821Aligned core viewer