Measured experimental coordinates · Phase 6C.1
7MDN · NSD2 PWWP1
Source chain E, canonical annotation-core residues 222–286. X-RAY DIFFRACTION · reported 2.42 Å. Original-coordinate SHA-256: 411eea421108aa7f0e46d8c191904297040016aeabc0f48ef43d4a7503888c2a.
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 | 14 | 14 | 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.
Y6V · calculated observed ligand environment
Deposited instance PDB:7MDN:LIG:M:Y6V:401:.. Closest calculated PWWP-region atom distance: 3.5464 Å. Five-Å native core contacts: 1; broader-Pfam contacts: 3; source-coordinate model 1.
Limitations: multi chain environment source annotation
| Canonical residue | Region | Protein atom | Ligand atom | Distance (Å) | Occupancy |
|---|---|---|---|---|---|
| 269 ASP | native annotation core | OD2 | C6 | 3.8855 | 1.0 / 1.0 |
| 317 LYS | broader pfam outside annotation core | CD | O1 | 3.7286 | 1.0 / 1.0 |
| 320 ALA | broader pfam outside annotation core | CB | C5 | 3.5464 | 1.0 / 1.0 |
| 321 GLN | broader pfam outside annotation core | NE2 | C6 | 4.2001 | 1.0 / 1.0 |
Y6V · calculated observed ligand environment
Deposited instance PDB:7MDN:LIG:N:Y6V:401:.. Closest calculated PWWP-region atom distance: 2.9125 Å. Five-Å native core contacts: 13; broader-Pfam contacts: 2; source-coordinate model 1.
Limitations: multi chain environment source annotation
| Canonical residue | Region | Protein atom | Ligand atom | Distance (Å) | Occupancy |
|---|---|---|---|---|---|
| 228 SER | native annotation core | O | C9 | 5.4356 | 1.0 / 1.0 |
| 229 LYS | native annotation core | C | C9 | 5.9503 | 1.0 / 1.0 |
| 230 VAL | native annotation core | CG2 | C9 | 3.6467 | 1.0 / 1.0 |
| 233 TYR | native annotation core | OH | O1 | 3.1881 | 1.0 / 1.0 |
| 234 PRO | native annotation core | O | C8 | 4.8902 | 1.0 / 1.0 |
| 236 TRP | native annotation core | CE3 | C8 | 3.5898 | 1.0 / 1.0 |
| 266 PHE | native annotation core | CB | O3 | 3.3232 | 1.0 / 1.0 |
| 267 PHE | native annotation core | O | C15 | 3.3185 | 1.0 / 1.0 |
| 268 GLY | native annotation core | CA | O2 | 3.2011 | 1.0 / 1.0 |
| 269 ASP | native annotation core | N | O2 | 3.3283 | 1.0 / 1.0 |
| 270 ALA | native annotation core | O | C14 | 2.9125 | 1.0 / 1.0 |
| 271 PRO | native annotation core | CA | C15 | 4.182 | 1.0 / 1.0 |
| 272 GLU | native annotation core | CG | C17 | 3.4871 | 1.0 / 1.0 |
| 273 ARG | native annotation core | O | C6 | 3.6056 | 1.0 / 1.0 |
| 274 ALA | native annotation core | CB | C5 | 3.6529 | 1.0 / 1.0 |
| 276 ILE | native annotation core | CD1 | C4 | 5.6736 | 1.0 / 1.0 |
| 318 LEU | broader pfam outside annotation core | CD1 | C12 | 3.8128 | 1.0 / 1.0 |
| 321 GLN | broader pfam outside annotation core | OE1 | N2 | 2.9491 | 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 / 12 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 223 / 13 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 224 / 14 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 225 / 15 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 226 / 16 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 227 / 17 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 228 / 18 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 229 / 19 | LYS | Yes | — | NZ | NZ | —; occupancy ≥ 1.0 |
| 230 / 20 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 231 / 21 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 232 / 22 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 233 / 23 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 234 / 24 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 235 / 25 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 236 / 26 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 237 / 27 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 238 / 28 | CYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 239 / 29 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 240 / 30 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 241 / 31 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 242 / 32 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 243 / 33 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 244 / 34 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 245 / 35 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 246 / 36 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 247 / 37 | HIS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 248 / 38 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 249 / 39 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 250 / 40 | THR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 251 / 41 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 252 / 42 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 253 / 43 | LYS | Yes | — | NZ | NZ | —; occupancy ≥ 1.0 |
| 254 / 44 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 255 / 45 | GLN | No coordinates | — | — | — | — |
| 256 / 46 | LYS | No coordinates | — | — | — | — |
| 257 / 47 | LYS | No coordinates | — | — | — | — |
| 258 / 48 | SER | Yes | — | OG | OG | —; occupancy ≥ 1.0 |
| 259 / 49 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 260 / 50 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 261 / 51 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 262 / 52 | TYR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 263 / 53 | HIS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 264 / 54 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 265 / 55 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 266 / 56 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 267 / 57 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 268 / 58 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 269 / 59 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 270 / 60 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 271 / 61 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 272 / 62 | GLU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 273 / 63 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 274 / 64 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 275 / 65 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 276 / 66 | ILE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 277 / 67 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 278 / 68 | GLU | Yes | — | CD, CG, OE1, OE2 | CD, CG, OE1, OE2 | —; occupancy ≥ 1.0 |
| 279 / 69 | LYS | Yes | — | CD, CE, NZ | CD, CE, NZ | —; occupancy ≥ 1.0 |
| 280 / 70 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 281 / 71 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 282 / 72 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 283 / 73 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 284 / 74 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 285 / 75 | GLU | Yes | — | CD, CG, OE1, OE2 | CD, CG, OE1, OE2 | —; occupancy ≥ 1.0 |
| 286 / 76 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
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