Measured experimental coordinates · Phase 6C.1
9Y60 · NSD2 PWWP1
Source chain A, canonical annotation-core residues 222–286. X-RAY DIFFRACTION · reported 2.023 Å. Original-coordinate SHA-256: 9ef0f36f9163b9d77a33b0955701d6fc233d3a9e69ec6c18caa65da3ed3e1df2.
Open deposited-coordinate molecular viewer Protein/domain context Original PDB entry
Model-aware structural assessment
Counts concern the annotated PWWP core. Different NMR models are evaluated independently, without averaging their coordinates into an artificial model.
| Model | Core residues observed | Missing backbone | Missing side-chain (union) | Missing side-chain (consistent conformer) | Partial occupancy residues | Unassessable chemistry |
|---|---|---|---|---|---|---|
| 1 | 65 | 0 | 16 | 16 | 0 | 0 |
Experimental ligand environments
Only separately source-classified research ligands are listed. Native annotation-core contacts and broader Pfam-fold contacts are identified separately. A simple distance is not an experimental affinity or density-quality score.
A1CSP · calculated observed ligand environment
Deposited instance PDB:9Y60:LIG:B:A1CSP:4000:.. Closest calculated PWWP-region atom distance: 2.8833 Å. Five-Å native core contacts: 12; broader-Pfam contacts: 2; source-coordinate model 1.
| Canonical residue | Region | Protein atom | Ligand atom | Distance (Å) | Occupancy |
|---|---|---|---|---|---|
| 228 SER | native annotation core | O | CL2 | 4.7258 | 1.0 / 1.0 |
| 229 LYS | native annotation core | C | CL2 | 5.8016 | 1.0 / 1.0 |
| 230 VAL | native annotation core | CG2 | CL2 | 3.7584 | 1.0 / 1.0 |
| 233 TYR | native annotation core | CB | CL2 | 3.4062 | 1.0 / 1.0 |
| 234 PRO | native annotation core | O | CL2 | 4.4386 | 1.0 / 1.0 |
| 236 TRP | native annotation core | CZ2 | N1 | 3.298 | 1.0 / 1.0 |
| 266 PHE | native annotation core | CB | O2 | 3.3081 | 1.0 / 1.0 |
| 267 PHE | native annotation core | O | C8 | 3.5743 | 1.0 / 1.0 |
| 268 GLY | native annotation core | CA | O1 | 3.3435 | 1.0 / 1.0 |
| 269 ASP | native annotation core | N | O1 | 3.3302 | 1.0 / 1.0 |
| 270 ALA | native annotation core | N | O1 | 2.8833 | 1.0 / 1.0 |
| 271 PRO | native annotation core | N | O1 | 4.474 | 1.0 / 1.0 |
| 272 GLU | native annotation core | CG | C1 | 3.5452 | 1.0 / 1.0 |
| 318 LEU | broader pfam outside annotation core | CD1 | C9 | 3.7684 | 1.0 / 1.0 |
| 321 GLN | broader pfam outside annotation core | OE1 | N1 | 2.8938 | 1.0 / 1.0 |
Residue-level coordinate and atom completeness
"Missing" applies only to residues with observed atoms and supported chemical templates. Unobserved residues are reported separately. Alternate-conformer union presence is distinct from a single internally consistent conformer.
| Canonical / entity position | Component | Observed | Missing backbone | Missing side-chain (union) | Missing side-chain (consistent) | Alt & occupancy |
|---|---|---|---|---|---|---|
| 222 / 22 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 223 / 23 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 224 / 24 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 225 / 25 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 226 / 26 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 227 / 27 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 228 / 28 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 229 / 29 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 230 / 30 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 231 / 31 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 232 / 32 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 233 / 33 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 234 / 34 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 235 / 35 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 236 / 36 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 237 / 37 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 238 / 38 | CYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 239 / 39 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 240 / 40 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 241 / 41 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 242 / 42 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 243 / 43 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 244 / 44 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 245 / 45 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 246 / 46 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 247 / 47 | HIS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 248 / 48 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 249 / 49 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 250 / 50 | THR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 251 / 51 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 252 / 52 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 253 / 53 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 254 / 54 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 255 / 55 | GLN | Yes | — | CD, CG, NE2, OE1 | CD, CG, NE2, OE1 | —; occupancy ≥ 1.0 |
| 256 / 56 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 257 / 57 | LYS | Yes | — | CD, CE, CG, NZ | CD, CE, CG, NZ | —; occupancy ≥ 1.0 |
| 258 / 58 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 259 / 59 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 260 / 60 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 261 / 61 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 262 / 62 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 263 / 63 | HIS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 264 / 64 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 265 / 65 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 266 / 66 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 267 / 67 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 268 / 68 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 269 / 69 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 270 / 70 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 271 / 71 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 272 / 72 | GLU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 273 / 73 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 274 / 74 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 275 / 75 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 276 / 76 | ILE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 277 / 77 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 278 / 78 | GLU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 279 / 79 | LYS | Yes | — | CD, CE, CG, NZ | CD, CE, CG, NZ | —; occupancy ≥ 1.0 |
| 280 / 80 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 281 / 81 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 282 / 82 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 283 / 83 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 284 / 84 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 285 / 85 | GLU | Yes | — | CD, CG, OE1, OE2 | CD, CG, OE1, OE2 | —; occupancy ≥ 1.0 |
| 286 / 86 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
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