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 · M3L
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 1093 | I:1093 · entity 20 · label I | annotation core | 4.4738 Å | Unassessed | |
| TYR 1096 | I:1096 · entity 23 · label I | annotation core | 3.3622 Å | Unassessed | |
| TYR 1099 | I:1099 · entity 26 · label I | annotation core | 3.7505 Å | Unassessed | |
| PHE 1147 | I:1147 · entity 74 · label I | annotation core | 3.6887 Å | Unassessed | |
| ASP 1149 | I:1149 · entity 76 · label I | annotation core | 3.6757 Å | Unassessed | |
| THR 1153 | I:1153 · entity 80 · label I | annotation core | 3.3033 Å | Unassessed | |
| TRP 1154 | I:1154 · entity 81 · label I | annotation core | 2.7424 Å | Unassessed | |
| GLN 1155 | I:1155 · entity 82 · label I | annotation core | 3.1708 Å | Unassessed | |
| ILE 1184 | I:1184 · entity 111 · label I | broader Pfam PWWP | 4.8455 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 |
|---|---|---|---|---|---|
| 2X35 · A | BRPF1 PWWP1 | 84 / 84 | 0 | Unassessed | — |
| 2X4W · A | BRPF1 PWWP1 | 84 / 84 | 2 | Unassessed | — |
| 2X4X · A | BRPF1 PWWP1 | 84 / 84 | 2 | Unassessed | — |
| 2X4X · C | BRPF1 PWWP1 | 84 / 84 | 1 | Unassessed | — |
| 2X4X · E | BRPF1 PWWP1 | 84 / 84 | 1 | Unassessed | — |
| 2X4X · G | BRPF1 PWWP1 | 84 / 84 | 1 | Unassessed | — |
| 2X4Y · A | BRPF1 PWWP1 | 84 / 84 | 4 | Unassessed | — |
| 2X4Y · C | BRPF1 PWWP1 | 84 / 84 | 3 | Unassessed | — |
| 2X4Y · E | BRPF1 PWWP1 | 84 / 84 | 2 | Unassessed | — |
| 2X4Y · G | BRPF1 PWWP1 | 84 / 84 | 2 | Unassessed | — |
| 2X4Y · I | BRPF1 PWWP1 | 84 / 84 | 1 | Unassessed | — |
| 2X4Y · K | BRPF1 PWWP1 | 84 / 84 | 1 | Unassessed | — |
| 2X4Y · M | BRPF1 PWWP1 | 84 / 84 | 1 | Unassessed | — |
| 2X4Y · O | BRPF1 PWWP1 | 84 / 84 | 2 | Unassessed | — |
| 3L42 · A | BRPF1 PWWP1 | 84 / 84 | 3 | Unassessed | — |
| 3MO8 · A | BRPF1 PWWP1 | 84 / 84 | 1 | Unassessed | — |
| 5C6S · A | BRPF1 PWWP1 | 84 / 84 | 17 | 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: d176722770f62d8382f5a0ecad813969c335bbf99bff85449860bfe2d67c59b7
Source PDB: https://www.rcsb.org/structure/2X4Y. 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.