Phase 6C.1 · Original deposited experimental coordinates
Comprehensive structure quality
Residue and heavy-atom completeness calculated directly from 230 source PDBx/mmCIF files, each verified against its frozen historical checksum. Each mapped PWWP chain/domain, NMR model and qualified source-supported ligand environment is tracked individually.
Experimental-coordinate case studies
Inspect actual examples
9FOC · NSD2 PWWP1
Newly assessed ligand-bearing structure
Protein and bound ligand coordinates are deposited, but the literature's assayed compound 11 preparation remains stereochemically unresolved. Structural components do not fix that ambiguity.
Inspect 9FOC completeness and ligands2M16 · PSIP1 PWWP
Deposited NMR ensemble
All model-specific atom observations are retained. Ensemble variation is not represented by a single first-model structure alone.
Inspect model coverage11OA · DNMT3A PWWP1
Independently confirmed side-chain gaps
Five observed-core chains each lack 198 standard side-chain heavy atoms; 13 other mapped chains contain no observed core coordinates.
Inspect exact missing atomsAnalyze family-wide experimental binding-site differences →
All 666 original chain/domain mappings
Search structural evidence
666 matching chain/domain records. Filters must be satisfied by the same experimental chain/domain. Model-specific assessment is available within each detail record.
| PDB · chain | Target/domain | Core observed | Experiment | Missing side-chain atoms | Backbone gaps | Research ligand environments | Assessment |
|---|---|---|---|---|---|---|---|
| 11NZ · A | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 4.19 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11NZ · B | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 4.19 Å | 198 | 0 | 0 | atomic completeness calculated |
| 11NZ · C | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 4.19 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11NZ · D | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 4.19 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11NZ · E | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 4.19 Å | 52 | 0 | 0 | atomic completeness calculated |
| 11NZ · F | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 4.19 Å | 52 | 0 | 0 | atomic completeness calculated |
| 11NZ · G | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 4.19 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11NZ · H | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 4.19 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11NZ · I | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 4.19 Å | 198 | 0 | 0 | atomic completeness calculated |
| 11NZ · J | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 4.19 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · A | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · B | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · C | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 5.04 Å | 198 | 0 | 0 | atomic completeness calculated |
| 11OA · D | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · E | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · F | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 5.04 Å | 198 | 0 | 0 | atomic completeness calculated |
| 11OA · G | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 5.04 Å | 198 | 0 | 0 | atomic completeness calculated |
| 11OA · H | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · I | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · J | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · K | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · L | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · M | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · N | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 5.04 Å | 198 | 0 | 0 | atomic completeness calculated |
| 11OA · O | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 5.04 Å | 198 | 0 | 0 | atomic completeness calculated |
| 11OA · P | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · Q | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OA · R | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 5.04 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OH · A | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 3.58 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OH · B | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 3.58 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OH · C | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 3.58 Å | 6 | 0 | 0 | atomic completeness calculated |
| 11OH · D | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 3.58 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OI · A | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 3.66 Å | 6 | 0 | 0 | atomic completeness calculated |
| 11OI · B | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 3.66 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OI · C | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 3.66 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OI · D | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 3.66 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OI · E | DNMT3A PWWP1 | 0 / 59 | ELECTRON MICROSCOPY · 3.66 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 11OI · F | DNMT3A PWWP1 | 59 / 59 | ELECTRON MICROSCOPY · 3.66 Å | 198 | 0 | 0 | atomic completeness calculated |
| 1H3Z · A | pdp2 PWWP1 | 65 / 65 | SOLUTION NMR · 23 models | 0 | 0 | 0 | atomic completeness calculated |
| 1KHC · A | Dnmt3b PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 1.8 Å | 9 | 0 | 0 | atomic completeness calculated |
| 1N27 · A | Hdgfl3 PWWP1 | 58 / 58 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 1RI0 · A | HDGF PWWP1 | 58 / 58 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 29HG · B | NSD2 PWWP1 | 65 / 65 | ELECTRON MICROSCOPY · 4.0 Å | 19 | 0 | 1 | atomic completeness calculated |
| 29HG · B | NSD2 PWWP2 | 0 / 63 | ELECTRON MICROSCOPY · 4.0 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 29HH · B | NSD2 PWWP1 | 65 / 65 | ELECTRON MICROSCOPY · 4.2 Å | 19 | 0 | 1 | atomic completeness calculated |
| 29HH · B | NSD2 PWWP2 | 0 / 63 | ELECTRON MICROSCOPY · 4.2 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 29HI · B | NSD2 PWWP1 | 65 / 65 | ELECTRON MICROSCOPY · 5.9 Å | 19 | 0 | 1 | atomic completeness calculated |
| 29HI · B | NSD2 PWWP2 | 0 / 63 | ELECTRON MICROSCOPY · 5.9 Å | Core not observed | 0 | 0 | domain not observed in deposit |
| 2B8A · A | Hdgf PWWP1 | 58 / 58 | SOLUTION NMR · 26 models | 0 | 0 | 0 | atomic completeness calculated |
| 2DAQ · A | NSD3 PWWP2 | 63 / 63 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 2GFU · A | MSH6 PWWP1 | 63 / 63 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 2L89 · A | pdp1 PWWP1 | 63 / 63 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 2M16 · A | PSIP1 PWWP1 | 64 / 64 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 2NAS · A | 28H13_90 PWWP1 | 62 / 62 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 2NLU · A | HDGF PWWP1 | 58 / 58 | SOLUTION NMR · 16 models | 0 | 0 | 0 | atomic completeness calculated |
| 2NLU · B | HDGF PWWP1 | 58 / 58 | SOLUTION NMR · 16 models | 0 | 0 | 0 | atomic completeness calculated |
| 2X35 · A | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 2.0 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4W · A | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.5 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4X · A | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.85 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4X · C | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.85 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4X · E | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.85 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4X · G | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.85 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4Y · A | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.7 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4Y · C | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.7 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4Y · E | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.7 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4Y · G | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.7 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4Y · I | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.7 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4Y · K | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.7 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4Y · M | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.7 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2X4Y · O | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.7 Å | 0 | 0 | 0 | atomic completeness calculated |
| 2YRV · A | ARID4A PWWP1 | 93 / 93 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 3EAE · A | HDGFL2 PWWP1 | 58 / 58 | X-RAY DIFFRACTION · 2.24 Å | 7 | 0 | 0 | atomic completeness calculated |
| 3EAE · B | HDGFL2 PWWP1 | 47 / 58 | X-RAY DIFFRACTION · 2.24 Å | 16 | 0 | 0 | atomic completeness calculated |
| 3FLG · A | DNMT3B PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 1.8 Å | 4 | 0 | 0 | atomic completeness calculated |
| 3L42 · A | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.3 Å | 32 | 0 | 0 | atomic completeness calculated |
| 3LLR · A | DNMT3A PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.3 Å | 0 | 0 | 0 | atomic completeness calculated |
| 3LLR · B | DNMT3A PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.3 Å | 0 | 0 | 0 | atomic completeness calculated |
| 3LLR · C | DNMT3A PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.3 Å | 0 | 0 | 0 | atomic completeness calculated |
| 3LLR · D | DNMT3A PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.3 Å | 0 | 0 | 0 | atomic completeness calculated |
| 3LLR · E | DNMT3A PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.3 Å | 0 | 0 | 0 | atomic completeness calculated |
| 3LYI · A | BRD1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 2.1 Å | 0 | 0 | 0 | atomic completeness calculated |
| 3LYI · B | BRD1 PWWP1 | 69 / 84 | X-RAY DIFFRACTION · 2.1 Å | 0 | 0 | 0 | atomic completeness calculated |
| 3MO8 · A | BRPF1 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.69 Å | 4 | 0 | 0 | atomic completeness calculated |
| 3PFS · A | BRPF3 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.9 Å | 10 | 0 | 0 | atomic completeness calculated |
| 3PFS · B | BRPF3 PWWP1 | 84 / 84 | X-RAY DIFFRACTION · 1.9 Å | 10 | 0 | 0 | atomic completeness calculated |
| 3PMI · A | PWWP3A PWWP1 | 62 / 62 | X-RAY DIFFRACTION · 2.82 Å | 48 | 0 | 0 | atomic completeness calculated with chemistry limitations |
| 3PMI · B | PWWP3A PWWP1 | 62 / 62 | X-RAY DIFFRACTION · 2.82 Å | 24 | 0 | 0 | atomic completeness calculated with chemistry limitations |
| 3PMI · C | PWWP3A PWWP1 | 62 / 62 | X-RAY DIFFRACTION · 2.82 Å | 31 | 0 | 0 | atomic completeness calculated with chemistry limitations |
| 3PMI · D | PWWP3A PWWP1 | 62 / 62 | X-RAY DIFFRACTION · 2.82 Å | 36 | 0 | 0 | atomic completeness calculated with chemistry limitations |
| 3QBY · A | HDGFL2 PWWP1 | 58 / 58 | X-RAY DIFFRACTION · 1.95 Å | 5 | 0 | 0 | atomic completeness calculated |
| 3QBY · B | HDGFL2 PWWP1 | 51 / 58 | X-RAY DIFFRACTION · 1.95 Å | 3 | 0 | 0 | atomic completeness calculated |
| 3QBY · C | HDGFL2 PWWP1 | 49 / 58 | X-RAY DIFFRACTION · 1.95 Å | 11 | 0 | 0 | atomic completeness calculated |
| 3QJ6 · A | HDGFL2 PWWP1 | 56 / 58 | X-RAY DIFFRACTION · 2.3 Å | 7 | 0 | 0 | atomic completeness calculated |
| 3QKJ · A | DNMT3B PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.04 Å | 4 | 0 | 0 | atomic completeness calculated |
| 3QKJ · B | DNMT3B PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.04 Å | 6 | 0 | 0 | atomic completeness calculated |
| 3QKJ · C | DNMT3B PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.04 Å | 10 | 0 | 0 | atomic completeness calculated |
| 3QKJ · D | DNMT3B PWWP1 | 59 / 59 | X-RAY DIFFRACTION · 2.04 Å | 6 | 0 | 0 | atomic completeness calculated |
| 3ZEH · A | PSIP1 PWWP1 | 62 / 64 | SOLUTION NMR · 20 models | 0 | 0 | 0 | atomic completeness calculated |
| 4COS · A | ZMYND8 PWWP1 | 51 / 51 | X-RAY DIFFRACTION · 1.67 Å | 0 | 0 | 0 | atomic completeness calculated |
| 4FU6 · A | PSIP1 PWWP1 | 62 / 64 | X-RAY DIFFRACTION · 2.1 Å | 18 | 2 | 0 | atomic completeness calculated |
Reproducible scientific exports
Individual experimental mmCIF files are verified by their original SHA-256. Core coordinates, standard heavy-atom templates and source UniProt mappings are analyzed model-by-model. Union-of-alternates and conformer-consistent completeness are distinct; 5 Å and 6 Å geometric proximity are not equivalent to a validated interaction.