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 · ZN
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 |
|---|---|---|---|---|---|
| CYS 490 | b:470 · entity 280 · label S | outside PWWP annotations | 2.4441 Å | Unassessed | |
| ASN 492 | b:472 · entity 282 · label S | outside PWWP annotations | 3.9521 Å | Unassessed | |
| CYS 495 | b:475 · entity 285 · label S | outside PWWP annotations | 2.0865 Å | Unassessed | |
| CYS 496 | b:476 · entity 286 · label S | outside PWWP annotations | 3.9493 Å | Unassessed | |
| ARG 497 | b:477 · entity 287 · label S | outside PWWP annotations | 4.6251 Å | Unassessed | |
| CYS 524 | b:504 · entity 314 · label S | outside PWWP annotations | 2.3968 Å | Unassessed | |
| CYS 527 | b:507 · entity 317 · label S | outside PWWP annotations | 2.4563 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 |
|---|---|---|---|---|---|
| 3FLG · A | DNMT3B PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 3QKJ · A | DNMT3B PWWP1 | 59 / 59 | 4 | Unassessed | — |
| 3QKJ · B | DNMT3B PWWP1 | 59 / 59 | 3 | Unassessed | — |
| 3QKJ · C | DNMT3B PWWP1 | 59 / 59 | 1 | Unassessed | — |
| 3QKJ · D | DNMT3B PWWP1 | 59 / 59 | 5 | Unassessed | — |
| 5CIU · A | DNMT3B PWWP1 | 59 / 59 | 1 | Unassessed | — |
| 5CIU · B | DNMT3B PWWP1 | 59 / 59 | 2 | Unassessed | — |
| 5NR3 · A | DNMT3B PWWP1 | 59 / 59 | 4 | Unassessed | — |
| 5NR3 · B | DNMT3B PWWP1 | 59 / 59 | 2 | Unassessed | — |
| 5NRR · A | DNMT3B PWWP1 | 59 / 59 | 5 | Unassessed | — |
| 5NRR · B | DNMT3B PWWP1 | 59 / 59 | 4 | Unassessed | — |
| 5NRS · A | DNMT3B PWWP1 | 59 / 59 | 4 | Unassessed | — |
| 5NRS · B | DNMT3B PWWP1 | 59 / 59 | 5 | Unassessed | — |
| 5NRV · A | DNMT3B PWWP1 | 59 / 59 | 7 | Unassessed | — |
| 5NRV · B | DNMT3B PWWP1 | 59 / 59 | 7 | Unassessed | — |
| 5NV0 · A | DNMT3B PWWP1 | 59 / 59 | 7 | Unassessed | — |
| 5NV0 · B | DNMT3B PWWP1 | 59 / 59 | 8 | Unassessed | — |
| 5NV2 · A | DNMT3B PWWP1 | 59 / 59 | 7 | Unassessed | — |
| 5NV2 · B | DNMT3B PWWP1 | 59 / 59 | 6 | Unassessed | — |
| 5NV7 · A | DNMT3B PWWP1 | 59 / 59 | 4 | Unassessed | — |
| 5NV7 · B | DNMT3B PWWP1 | 59 / 59 | 5 | Unassessed | — |
| 5NVO · A | DNMT3B PWWP1 | 59 / 59 | 8 | Unassessed | — |
| 5NVO · B | DNMT3B PWWP1 | 59 / 59 | 7 | Unassessed | — |
| 6PA7 · L | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 6PA7 · N | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 6R3E · A | DNMT3B PWWP1 | 59 / 59 | 4 | Unassessed | — |
| 6R3E · B | DNMT3B PWWP1 | 59 / 59 | 1 | Unassessed | — |
| 8EIH · A | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIH · B | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIH · C | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIH · D | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIH · E | DNMT3B PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 8EII · A | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EII · B | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EII · C | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EII · D | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIJ · A | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIJ · B | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIJ · C | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIK · A | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIK · B | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIK · C | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIK · D | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIK · E | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8EIK · F | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 8ZLK · A | DNMT3B PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 8ZLK · B | DNMT3B PWWP1 | 59 / 59 | 0 | Unassessed | — |
| 9E00 · S | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E00 · T | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E00 · W | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E00 · X | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E05 · S | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E05 · T | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E05 · W | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E05 · X | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E0F · A | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E0F · B | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E0G · A | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E0G · B | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2D · Q | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2D · R | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2D · U | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2D · V | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2Q · S | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2Q · T | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2Q · W | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2Q · X | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2R · S | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2R · T | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2R · W | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E2R · X | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3D · S | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3D · T | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3R · S | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3R · T | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3R · W | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3R · X | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3U · I | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3U · L | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9E3U · M | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9Q7U · K | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9Q7U · L | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9Y4P · S | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9Y4P · T | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9Y4P · W | DNMT3B PWWP1 | 0 / 59 | 0 | Unassessed | — |
| 9Y4P · X | DNMT3B 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: 533eed738f27d838756d10676bb071c61e52b60f6413fe2e036501b162854d9e
Source PDB: https://www.rcsb.org/structure/9Y4P. 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.