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.
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Atom completeness · selected chain and annotation core
What can these coordinates support?
Construct substitutions, alternate conformers and interpretation
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.
Source-recorded construct sequence mismatches: [{"construct": "H", "entity_position": 603, "reference": "R", "uniprot_position": 882}]. Observed core substitutions: [].
Core residues with alternate conformers: 0. Alternate-specific completeness is retained in the selected JSON export. Missing coordinates have not been filled.
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 537 | C:537 · entity 258 · label C | outside PWWP annotations | 2.3323 Å | Standard atoms present | |
| ILE 539 | C:539 · entity 260 · label C | outside PWWP annotations | 4.3938 Å | Standard atoms present | |
| CYS 540 | C:540 · entity 261 · label C | outside PWWP annotations | 2.3219 Å | Standard atoms present | |
| CYS 541 | C:541 · entity 262 · label C | outside PWWP annotations | 4.8958 Å | Standard atoms present | |
| GLY 542 | C:542 · entity 263 · label C | outside PWWP annotations | 4.3005 Å | Standard atoms present | |
| CYS 559 | C:559 · entity 280 · label C | outside PWWP annotations | 2.3161 Å | Standard atoms present | |
| CYS 562 | C:562 · entity 283 · label C | outside PWWP annotations | 2.3286 Å | Standard atoms present |
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: 22b69191b56482b52a2cc8a8a6f517b143b90300e647239a8ef53c45b3c5873c
Source PDB: https://www.rcsb.org/structure/11OA. 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.