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?
Construct substitutions, alternate conformers and interpretation
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.
Source-recorded construct sequence mismatches: []. Observed core substitutions: [].
Core residues with alternate conformers: 1. Alternate-specific completeness is retained in the selected JSON export. Missing coordinates have not been filled.
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 · V01
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 230 | A:230 · entity 21 · label A | annotation core | 3.8951 Å | Standard atoms present | |
| TYR 233 | A:233 · entity 24 · label A | annotation core | 3.3246 Å | Standard atoms present | |
| TRP 236 | A:236 · entity 27 · label A | annotation core | 3.5457 Å | Standard atoms present | |
| PHE 266 | A:266 · entity 57 · label A | annotation core | 3.1885 Å | Standard atoms present | |
| PHE 267 | A:267 · entity 58 · label A | annotation core | 3.3736 Å | Standard atoms present | |
| GLY 268 | A:268 · entity 59 · label A | annotation core | 3.1722 Å | Standard atoms present | |
| ASP 269 | A:269 · entity 60 · label A | annotation core | 3.2062 Å | Standard atoms present | |
| ALA 270 | A:270 · entity 61 · label A | annotation core | 2.8613 Å | Standard atoms present | |
| PRO 271 | A:271 · entity 62 · label A | annotation core | 4.3291 Å | Standard atoms present | |
| GLU 272 | A:272 · entity 63 · label A | annotation core | 3.0201 Å | Standard atoms present | |
| ARG 273 | A:273 · entity 64 · label A | annotation core | 3.0145 Å | Standard atoms present | |
| ALA 274 | A:274 · entity 65 · label A | annotation core | 3.6628 Å | Standard atoms present | |
| TRP 275 | A:275 · entity 66 · label A | annotation core | 4.5773 Å | Standard atoms present | |
| LEU 318 | A:318 · entity 109 · label A | broader Pfam PWWP | 3.4573 Å | Standard atoms present | |
| GLN 321 | A:321 · entity 112 · label A | broader Pfam PWWP | 2.8670 Å | Standard atoms present |
Identity, native target and exact site links
Linked experimental assays
| Measured preparation | Method / endpoint | Original observation | Tested construct | Evidence |
|---|---|---|---|---|
| UNC6934 | SPR Kd · | = 91.0 nM | 208–368 | PWWP:ASSAY:0004 same exact chemical identity and native domain; construct equivalence not assumed |
| UNC6934 | AlphaScreen IC50 · | = 104.0 nM | 208–368 | PWWP:ASSAY:0005 same exact chemical identity and native domain; construct equivalence not assumed |
| UNC6934 | NanoBRET PPI half-response · | = 1.23 µM | Unknown–Unknown | PWWP:ASSAY:0006 same exact chemical identity and native domain; construct equivalence not assumed |
| UNC6934 | SPR Kd · | = 0.24 µM | 208–368 | PWWP:ASSAY:0014 same exact chemical identity and native domain; construct equivalence not assumed |
| UNC6934 | SPR Kd · | = 1.33 µM | 211–350 | PWWP:ASSAY:0021 same exact chemical identity and native domain; construct equivalence not assumed |
Filterable structural assessment inventory
Coordinate coverage & quality
| PDB / chain | Domain | Core Cα coverage | PWWP-contact ligand instances | Atom assessment | Missing core heavy atoms |
|---|---|---|---|---|---|
| 6XCG · A | NSD2 PWWP1 | 65 / 65 | 1 | Assessed | 6 |
| 6XCG · B | NSD2 PWWP1 | 65 / 65 | 4 | Assessed | 12 |
| 6XCG · C | NSD2 PWWP1 | 63 / 65 | 5 | Assessed | 4 |
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: 2c370701c9b83de7ae6137f91d2130519a48c261a93ec5bc480dfcc3bc982200
Source PDB: https://www.rcsb.org/structure/6XCG. 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.