Measured experimental coordinates · Phase 6C.1
9KNA · NSD2 PWWP1
Source chain B, canonical annotation-core residues 222–286. X-RAY DIFFRACTION · reported 2.92 Å. Original-coordinate SHA-256: 21757b20303ea68cd50bffdfa7659337c135d9e7492ac4d656b0f3f865cfdacf.
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 | 62 | 0 | 9 | 9 | 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.
6Y3 · calculated observed ligand environment
Deposited instance PDB:9KNA:LIG:C:6Y3:401:.. Closest calculated PWWP-region atom distance: 3.3457 Å. Five-Å native core contacts: 1; broader-Pfam contacts: 0; source-coordinate model 1.
Limitations: multi chain environment source annotation
| Canonical residue | Region | Protein atom | Ligand atom | Distance (Å) | Occupancy |
|---|---|---|---|---|---|
| 245 LEU | native annotation core | O | N20 | 5.717 | 1.0 / 1.0 |
| 246 LEU | native annotation core | CD2 | N20 | 3.3457 | 1.0 / 1.0 |
6Y3 · calculated observed ligand environment
Deposited instance PDB:9KNA:LIG:I:6Y3:401:.. Closest calculated PWWP-region atom distance: 2.2362 Å. Five-Å native core contacts: 4; broader-Pfam contacts: 7; source-coordinate model 1.
Limitations: multi chain environment source annotation
| Canonical residue | Region | Protein atom | Ligand atom | Distance (Å) | Occupancy |
|---|---|---|---|---|---|
| 229 LYS | native annotation core | CE | SE07 | 5.9958 | 1.0 / 1.0 |
| 232 GLY | native annotation core | O | N20 | 3.2261 | 1.0 / 1.0 |
| 233 TYR | native annotation core | C | C18 | 3.9446 | 1.0 / 1.0 |
| 234 PRO | native annotation core | CB | O23 | 3.2867 | 1.0 / 1.0 |
| 235 TRP | native annotation core | N | SE07 | 4.5688 | 1.0 / 1.0 |
| 290 PHE | broader pfam outside annotation core | CZ | SE07 | 3.5417 | 1.0 / 1.0 |
| 294 CYS | broader pfam outside annotation core | SG | SE07 | 2.2362 | 1.0 / 1.0 |
| 310 LEU | broader pfam outside annotation core | CD2 | O23 | 3.1784 | 1.0 / 1.0 |
| 312 LYS | broader pfam outside annotation core | O | N15 | 3.0385 | 1.0 / 1.0 |
| 313 PRO | broader pfam outside annotation core | O | C22 | 3.7845 | 1.0 / 1.0 |
| 314 ILE | broader pfam outside annotation core | CG1 | N15 | 3.0495 | 1.0 / 1.0 |
| 318 LEU | broader pfam outside annotation core | CD2 | C21 | 3.9207 | 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 / 6 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 223 / 7 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 224 / 8 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 225 / 9 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 226 / 10 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 227 / 11 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 228 / 12 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 229 / 13 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 230 / 14 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 231 / 15 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 232 / 16 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 233 / 17 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 234 / 18 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 235 / 19 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 236 / 20 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 237 / 21 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 238 / 22 | CYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 239 / 23 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 240 / 24 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 241 / 25 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 242 / 26 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 243 / 27 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 244 / 28 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 245 / 29 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 246 / 30 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 247 / 31 | HIS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 248 / 32 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 249 / 33 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 250 / 34 | THR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 251 / 35 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 252 / 36 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 253 / 37 | LYS | Yes | — | CD, CE, NZ | CD, CE, NZ | —; occupancy ≥ 1.0 |
| 254 / 38 | GLY | No coordinates | — | — | — | — |
| 255 / 39 | GLN | No coordinates | — | — | — | — |
| 256 / 40 | LYS | No coordinates | — | — | — | — |
| 257 / 41 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 258 / 42 | SER | Yes | — | CB, OG | CB, OG | —; occupancy ≥ 1.0 |
| 259 / 43 | ALA | Yes | — | CB | CB | —; occupancy ≥ 1.0 |
| 260 / 44 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 261 / 45 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 262 / 46 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 263 / 47 | HIS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 264 / 48 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 265 / 49 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 266 / 50 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 267 / 51 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 268 / 52 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 269 / 53 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 270 / 54 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 271 / 55 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 272 / 56 | GLU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 273 / 57 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 274 / 58 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 275 / 59 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 276 / 60 | ILE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 277 / 61 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 278 / 62 | GLU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 279 / 63 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 280 / 64 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 281 / 65 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 282 / 66 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 283 / 67 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 284 / 68 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 285 / 69 | GLU | Yes | — | CD, OE1, OE2 | CD, OE1, OE2 | —; occupancy ≥ 1.0 |
| 286 / 70 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
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