Measured experimental coordinates · Phase 6C.1
6R3E · DNMT3B PWWP1
Source chain A, canonical annotation-core residues 225–283. X-RAY DIFFRACTION · reported 2.269 Å. Original-coordinate SHA-256: f11f4e7bcd8a67152407442feee80117e2f1d3146e35bbce7e8eacb39e404552.
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 | 59 | 0 | 0 | 0 | 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.
96H · calculated observed ligand environment
Deposited instance PDB:6R3E:LIG:C:96H:501:.. Closest calculated PWWP-region atom distance: 2.3774 Å. Five-Å native core contacts: 7; broader-Pfam contacts: 0; source-coordinate model 1.
Limitations: partial occupancy contact atoms
| Canonical residue | Region | Protein atom | Ligand atom | Distance (Å) | Occupancy |
|---|---|---|---|---|---|
| 231 GLY | native annotation core | O | O01 | 5.472 | 1.0 / 0.94 |
| 233 ILE | native annotation core | CG1 | O01 | 3.9699 | 1.0 / 0.94 |
| 236 PHE | native annotation core | CE1 | C06 | 3.4411 | 1.0 / 0.94 |
| 237 SER | native annotation core | O | O01 | 4.9513 | 1.0 / 0.94 |
| 239 TRP | native annotation core | NE1 | C12 | 3.3189 | 1.0 / 0.94 |
| 240 PRO | native annotation core | O | C03 | 5.7914 | 1.0 / 0.94 |
| 263 TRP | native annotation core | CD2 | C03 | 3.3547 | 1.0 / 0.94 |
| 264 PHE | native annotation core | O | C12 | 4.6152 | 1.0 / 0.94 |
| 265 GLY | native annotation core | C | C12 | 5.3574 | 1.0 / 0.94 |
| 266 ASP | native annotation core | OD2 | O13 | 2.3774 | 1.0 / 0.94 |
| 268 LYS | native annotation core | NZ | O13 | 5.1348 | 1.0 / 0.94 |
| 270 SER | native annotation core | OG | C02 | 5.8349 | 1.0 / 0.94 |
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 |
|---|---|---|---|---|---|---|
| 225 / 11 | ILE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 226 / 12 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 227 / 13 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 228 / 14 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 229 / 15 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 230 / 16 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 231 / 17 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 232 / 18 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 233 / 19 | ILE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 234 / 20 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 235 / 21 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 236 / 22 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 237 / 23 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 238 / 24 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 239 / 25 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 240 / 26 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 241 / 27 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 242 / 28 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 243 / 29 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 244 / 30 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 245 / 31 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 246 / 32 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 247 / 33 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 248 / 34 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 249 / 35 | THR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 250 / 36 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 251 / 37 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 252 / 38 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 253 / 39 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 254 / 40 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 255 / 41 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 256 / 42 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 257 / 43 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 258 / 44 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 259 / 45 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 260 / 46 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 261 / 47 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 262 / 48 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 263 / 49 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 264 / 50 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 265 / 51 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 266 / 52 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 267 / 53 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 268 / 54 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 269 / 55 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 270 / 56 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 271 / 57 | GLU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 272 / 58 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 273 / 59 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 274 / 60 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 275 / 61 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 276 / 62 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 277 / 63 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 278 / 64 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 279 / 65 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 280 / 66 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 281 / 67 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 282 / 68 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 283 / 69 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
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