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 · OCS
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 937 | A:937 · entity 14 · label A | annotation core | 4.0798 Å | Unassessed | |
| TYR 940 | A:940 · entity 17 · label A | annotation core | 4.0745 Å | Unassessed | |
| TYR 943 | A:943 · entity 20 · label A | annotation core | 4.3395 Å | Unassessed | |
| PHE 991 | A:991 · entity 68 · label A | annotation core | 3.7568 Å | Unassessed | |
| ASP 993 | A:993 · entity 70 · label A | annotation core | 3.8984 Å | Unassessed | |
| SER 997 | A:997 · entity 74 · label A | annotation core | 3.7090 Å | Unassessed | |
| TRP 998 | A:998 · entity 75 · label A | annotation core | 3.7625 Å | Unassessed | |
| GLN 999 | A:999 · entity 76 · label A | annotation core | 3.3409 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 |
|---|---|---|---|---|---|
| 3LYI · A | BRD1 PWWP1 | 84 / 84 | 1 | Unassessed | — |
| 3LYI · B | BRD1 PWWP1 | 69 / 84 | 0 | Unassessed | — |
| 4Z02 · A | BRD1 PWWP1 | 84 / 84 | 9 | Unassessed | — |
| 4Z02 · B | BRD1 PWWP1 | 69 / 84 | 4 | Unassessed | — |
| 7LH9 · A | BRD1 PWWP1 | 74 / 84 | 0 | Unassessed | — |
| 7LH9 · B | BRD1 PWWP1 | 84 / 84 | 0 | Unassessed | — |
| 7LH9 · C | BRD1 PWWP1 | 71 / 84 | 0 | Unassessed | — |
| 7LH9 · D | BRD1 PWWP1 | 81 / 84 | 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: daab1f3e3c0ac65876a2031e90670a8d78fe37c492066102a302bc9d9a917097
Source PDB: https://www.rcsb.org/structure/3LYI. 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.