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?
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 255 | D:255 · entity 173 · label D | outside PWWP annotations | 2.1960 Å | Unassessed | |
| GLU 257 | D:257 · entity 175 · label D | outside PWWP annotations | 4.5261 Å | Unassessed | |
| CYS 258 | D:258 · entity 176 · label D | outside PWWP annotations | 2.3643 Å | Unassessed | |
| CYS 274 | D:274 · entity 192 · label D | outside PWWP annotations | 2.4257 Å | Unassessed | |
| HIS 278 | D:278 · entity 196 · label D | annotation core | 2.2224 Å | Unassessed | |
| LEU 296 | D:296 · entity 214 · label D | annotation core | 4.4432 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 |
|---|---|---|---|---|---|
| 4COS · A | ZMYND8 PWWP1 | 51 / 51 | 2 | Unassessed | — |
| 5B73 · A | ZMYND8 PWWP1 | 51 / 51 | 1 | Unassessed | — |
| 5Y1Z · C | ZMYND8 PWWP1 | 51 / 51 | 3 | Unassessed | — |
| 5Y1Z · D | ZMYND8 PWWP1 | 51 / 51 | 3 | Unassessed | — |
| 9T2F · A | ZMYND8 PWWP1 | 51 / 51 | 2 | Unassessed | — |
| 9T2G · A | ZMYND8 PWWP1 | 51 / 51 | 1 | 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: be13d6b91869c9f53cf8d4f56feeafd44b575e91a966831894aab4ceffbf73a3
Source PDB: https://www.rcsb.org/structure/5Y1Z. 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.