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 · EHQ
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 |
|---|---|---|---|---|---|
| VAL 278 | A:278 · entity 16 · label A | annotation core | 3.1603 Å | Unassessed | |
| TYR 281 | A:281 · entity 19 · label A | annotation core | 3.2658 Å | Unassessed | |
| TRP 284 | A:284 · entity 22 · label A | annotation core | 3.2932 Å | Unassessed | |
| PHE 312 | A:312 · entity 50 · label A | annotation core | 3.3801 Å | Unassessed | |
| SER 314 | A:314 · entity 52 · label A | annotation core | 2.7783 Å | Unassessed | |
| GLN 316 | A:316 · entity 54 · label A | annotation core | 3.2228 Å | Unassessed | |
| GLU 318 | A:318 · entity 56 · label A | annotation core | 3.4910 Å | Unassessed | |
| ARG 319 | A:319 · entity 57 · label A | annotation core | 4.0335 Å | Unassessed | |
| ALA 320 | A:320 · entity 58 · label A | annotation core | 3.8879 Å | Unassessed | |
| GLN 367 | A:367 · entity 105 · label A | broader Pfam PWWP | 3.8405 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 |
|---|---|---|---|---|---|
| 6G24 · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G25 · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G27 · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G29 · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G2B · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G2C · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G2E · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G2F · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G2O · A | NSD3 PWWP1 | 64 / 64 | 1 | Assessed | 0 |
| 6G3P · A | NSD3 PWWP1 | 64 / 64 | 0 | Unassessed | — |
| 6G3P · B | NSD3 PWWP1 | 64 / 64 | 0 | Unassessed | — |
| 6G3P · C | NSD3 PWWP1 | 64 / 64 | 0 | Unassessed | — |
| 6G3P · D | NSD3 PWWP1 | 64 / 64 | 0 | Unassessed | — |
| 6G3T · A | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G3T · B | NSD3 PWWP1 | 64 / 64 | 2 | Unassessed | — |
| 6G3T · C | NSD3 PWWP1 | 64 / 64 | 1 | Unassessed | — |
| 6G3T · D | NSD3 PWWP1 | 64 / 64 | 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: 5152ef05ba1370446f648a127c9d33cc6db9734edbe4d797a8958a18e6d64b14
Source PDB: https://www.rcsb.org/structure/6G25. 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.