Experimental coordinates · Exact deposited instances
Ligand contacts & pocket quality
Inspect the atoms that are present, the residues that are missing, and the precise scope of each chemical association.
Phase 6C historical atom / receptor assessment Phase 6C.1 full-atom experimental quality inventory
Full-coordinate Phase 6C.1 atom and ligand environment assessment
Load the checksum-verified original coordinates to explore the selected chain and ligand.
Drag to rotate · scroll to zoom · arrow keys rotate · + / − zoom · Home resets. Select a residue below to highlight its observed atoms.
Atom completeness · selected chain and annotation core
What can these coordinates support?
A fully observed annotation core is not a complete-receptor certification. Short annotation intervals, absent peripheral residues, alternate conformers and unexamined density can limit structural interpretation. No receptor preparation was performed.
Frozen 5 Å heavy-atom proximity observations
Contacting residues · SAH
Heavy-atom distances use the first deposited model and asymmetric unit, occupancy >0 and retained alternate locations. No symmetry expansion or affinity inference. Proximity alone is not evidence of affinity or a functional interaction.
| Canonical residue | Deposited residue | Scope | Minimum distance | Atom quality | Inspect |
|---|---|---|---|---|---|
| PHE 640 | W:640 · entity 417 · label Y | outside PWWP annotations | 3.0501 Å | Unassessed | |
| ASP 641 | W:641 · entity 418 · label Y | outside PWWP annotations | 3.4391 Å | Unassessed | |
| GLY 642 | W:642 · entity 419 · label Y | outside PWWP annotations | 4.2291 Å | Unassessed | |
| ILE 643 | W:643 · entity 420 · label Y | outside PWWP annotations | 3.7173 Å | Unassessed | |
| THR 645 | W:645 · entity 422 · label Y | outside PWWP annotations | 2.9937 Å | Unassessed | |
| SER 663 | W:663 · entity 440 · label Y | outside PWWP annotations | 3.7869 Å | Unassessed | |
| GLU 664 | W:664 · entity 441 · label Y | outside PWWP annotations | 3.0402 Å | Unassessed | |
| VAL 665 | W:665 · entity 442 · label Y | outside PWWP annotations | 3.8669 Å | Unassessed | |
| CYS 666 | W:666 · entity 443 · label Y | outside PWWP annotations | 3.5536 Å | Unassessed | |
| SER 669 | W:669 · entity 446 · label Y | outside PWWP annotations | 4.4682 Å | Unassessed | |
| GLY 685 | W:685 · entity 462 · label Y | outside PWWP annotations | 4.1178 Å | Unassessed | |
| ASP 686 | W:686 · entity 463 · label Y | outside PWWP annotations | 3.9605 Å | Unassessed | |
| VAL 687 | W:687 · entity 464 · label Y | outside PWWP annotations | 3.6241 Å | Unassessed | |
| GLY 707 | W:707 · entity 484 · label Y | outside PWWP annotations | 3.9514 Å | Unassessed | |
| PRO 709 | W:709 · entity 486 · label Y | outside PWWP annotations | 4.4408 Å | Unassessed | |
| LEU 730 | W:730 · entity 507 · label Y | outside PWWP annotations | 3.5727 Å | Unassessed | |
| GLU 756 | W:756 · entity 533 · label Y | outside PWWP annotations | 4.8082 Å | Unassessed | |
| LEU 888 | W:888 · entity 665 · label Y | outside PWWP annotations | 4.6047 Å | Unassessed | |
| ARG 891 | W:891 · entity 668 · label Y | outside PWWP annotations | 2.6992 Å | Unassessed | |
| SER 892 | W:892 · entity 669 · label Y | outside PWWP annotations | 3.1219 Å | Unassessed | |
| TRP 893 | W:893 · entity 670 · label Y | outside PWWP annotations | 2.6868 Å | Unassessed |
Identity, native target and exact site links
Linked experimental assays
| Measured preparation | Method / endpoint | Original observation | Tested construct | Evidence |
|---|---|---|---|---|
| No exact site-to-assay link is established in the frozen evidence graph. Visit the domain's Ligands & Bioactivity section for newly curated or structure-free observations. | ||||
Filterable structural assessment inventory
Coordinate coverage & quality
| PDB / chain | Domain | Core Cα coverage | PWWP-contact ligand instances | Atom assessment | Missing core heavy atoms |
|---|---|---|---|---|---|
| 11NZ · A | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11NZ · B | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 11NZ · C | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11NZ · D | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11NZ · E | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 11NZ · F | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 11NZ · G | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11NZ · H | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11NZ · I | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 11NZ · J | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11OA · A | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · B | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · C | DNMT3A PWWP1 | 59 / 59 | 0 | Assessed | 198 |
| 11OA · D | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · E | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · F | DNMT3A PWWP1 | 59 / 59 | 0 | Assessed | 198 |
| 11OA · G | DNMT3A PWWP1 | 59 / 59 | 0 | Assessed | 198 |
| 11OA · H | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · I | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · J | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · K | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · L | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · M | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · N | DNMT3A PWWP1 | 59 / 59 | 0 | Assessed | 198 |
| 11OA · O | DNMT3A PWWP1 | 59 / 59 | 0 | Assessed | 198 |
| 11OA · P | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · Q | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OA · R | DNMT3A PWWP1 | 0 / 59 | 0 | Assessed | 0 |
| 11OH · A | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11OH · B | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11OH · C | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 11OH · D | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11OI · A | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 11OI · B | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11OI · C | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11OI · D | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11OI · E | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 11OI · F | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 3LLR · A | DNMT3A PWWP1 | 59 / 59 | 1 | Unassessed | — |
| 3LLR · B | DNMT3A PWWP1 | 59 / 59 | 2 | Unassessed | — |
| 3LLR · C | DNMT3A PWWP1 | 59 / 59 | 1 | Unassessed | — |
| 3LLR · D | DNMT3A PWWP1 | 59 / 59 | 1 | Unassessed | — |
| 3LLR · E | DNMT3A PWWP1 | 59 / 59 | 1 | Unassessed | — |
| 6PA7 · K | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 6PA7 · M | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8QZM · K | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E00 · U | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E00 · V | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E00 · Y | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E00 · Z | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E05 · U | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E05 · V | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E05 · Y | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E05 · Z | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E0F · C | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E0F · D | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E0G · C | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E0G · D | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E2D · S | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2D · T | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E2D · W | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2D · X | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E2Q · U | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2Q · V | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2Q · Y | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2Q · Z | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2R · U | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2R · V | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E2R · Y | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2R · Z | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E3D · U | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3D · V | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E3R · U | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3R · V | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3R · Y | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3R · Z | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3U · N | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3U · O | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9LQ1 · A | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9LQ1 · D | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MP0 · A | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MP0 · B | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MP0 · C | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MP0 · D | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MP0 · E | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MP0 · F | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MP0 · G | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MP0 · H | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MPO · A | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MPO · B | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MPO · C | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MPO · D | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MPO · E | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MPO · F | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MPP · K | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9MPP · M | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9PRW · A | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9PRW · D | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9Q7U · M | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9Q7U · N | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9Y4P · U | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9Y4P · V | DNMT3A PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9Y4P · Y | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9Y4P · Z | DNMT3A PWWP1 | 0 / 59 | 0 | Unassessed | — |
Source bytes, methods and provenance
Detailed atom completeness only for the three packaged original-coordinate files; quality uses observed atom-name union across positive-occupancy alternate conformers, with per-alt differences retained. Missing entire residues are separate. Nonstandard amino-acid templates are unassessed. No density reinterpretation, receptor repair, docking or MD.
Coordinate SHA-256: 01318429b9a7c29f14772a47afaec906a05fa64cc76271d5e88bc4d3f735ea10
Source PDB: https://www.rcsb.org/structure/9E00. Original coordinate file: mmCIF. Original annotation and contact calculations are retained unchanged; the additional completeness assessment is PWWP_POCKET_QUALITY_1.0.0.
Methods and reproducible builder are included under analysis/phase5_pockets and scripts/build_phase5_pockets.py in the downloadable release.