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 · UNX
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 |
|---|---|---|---|---|---|
| GLY 288 | A:288 · entity 70 · label A | annotation core | 2.5292 Å | Unassessed | |
| LEU 289 | A:289 · entity 71 · label A | annotation core | 4.7781 Å | Unassessed | |
| PHE 290 | A:290 · entity 72 · label A | annotation core | 4.5071 Å | Unassessed | |
| ALA 343 | A:343 · entity 125 · label A | outside PWWP annotations | 4.5845 Å | Unassessed | |
| GLY 346 | A:346 · entity 128 · label A | outside PWWP annotations | 3.9313 Å | Unassessed | |
| PHE 347 | A:347 · entity 129 · label A | outside PWWP annotations | 3.3618 Å | Unassessed | |
| ILE 352 | A:352 · entity 134 · label A | outside PWWP annotations | 3.1750 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 |
|---|---|---|---|---|---|
| 1KHC · A | Dnmt3b PWWP1 | 59 / 59 | 20 | 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: 74e6ef75c14272818121a250f29daee64bb2485d0fdf784911795a3d408e79d7
Source PDB: https://www.rcsb.org/structure/1KHC. 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.