Measured experimental coordinates · Phase 6C.1
9KNB · NSD2 PWWP1
Source chain A, canonical annotation-core residues 222–286. X-RAY DIFFRACTION · reported 1.84 Å. Original-coordinate SHA-256: 7077f887135785974d1978ce67a4a1880b3fe422a584fcac87433458a1a301a1.
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 | 60 | 2 | 13 | 13 | 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.
A1EF7 · calculated observed ligand environment
Deposited instance PDB:9KNB:LIG:C:A1EF7:502:.. Closest calculated PWWP-region atom distance: 2.2308 Å. Five-Å native core contacts: 5; broader-Pfam contacts: 8; source-coordinate model 1.
| Canonical residue | Region | Protein atom | Ligand atom | Distance (Å) | Occupancy |
|---|---|---|---|---|---|
| 229 LYS | native annotation core | NZ | C12 | 3.9057 | 1.0 / 1.0 |
| 230 VAL | native annotation core | O | C13 | 5.6142 | 1.0 / 1.0 |
| 231 SER | native annotation core | C | C13 | 5.2743 | 1.0 / 1.0 |
| 232 GLY | native annotation core | O | C14 | 3.1342 | 1.0 / 1.0 |
| 233 TYR | native annotation core | N | C13 | 3.5839 | 1.0 / 1.0 |
| 234 PRO | native annotation core | CD | C17 | 3.6771 | 1.0 / 1.0 |
| 235 TRP | native annotation core | N | SE01 | 3.9867 | 1.0 / 1.0 |
| 290 PHE | broader pfam outside annotation core | CZ | C03 | 3.5772 | 1.0 / 1.0 |
| 294 CYS | broader pfam outside annotation core | SG | SE01 | 2.2308 | 1.0 / 1.0 |
| 310 LEU | broader pfam outside annotation core | O | C12 | 3.4264 | 1.0 / 1.0 |
| 311 LEU | broader pfam outside annotation core | CD1 | O18 | 3.2007 | 1.0 / 1.0 |
| 312 LYS | broader pfam outside annotation core | O | N09 | 3.0715 | 1.0 / 1.0 |
| 313 PRO | broader pfam outside annotation core | O | O16 | 3.5275 | 1.0 / 1.0 |
| 314 ILE | broader pfam outside annotation core | CD1 | C06 | 3.6119 | 1.0 / 1.0 |
| 318 LEU | broader pfam outside annotation core | CD2 | C17 | 3.5302 | 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 | — | CD2 | CD2 | —; 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 | No coordinates | — | — | — | — |
| 258 / 42 | SER | No coordinates | — | — | — | — |
| 259 / 43 | ALA | Yes | CA, N | 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 | — | OE1, OE2 | OE1, OE2 | —; occupancy ≥ 1.0 |
| 279 / 63 | LYS | Yes | — | CD, CE, NZ | CD, CE, NZ | —; 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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