Measured experimental coordinates · Phase 6C.1
5NV2 · DNMT3B PWWP1
Source chain A, canonical annotation-core residues 225–283. X-RAY DIFFRACTION · reported 2.029 Å. Original-coordinate SHA-256: 90c69902789421dcb9c6982f74df193641fd6d84bf5163de125de814878ab7b1.
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.
9AE · calculated observed ligand environment
Deposited instance PDB:5NV2:LIG:C:9AE:401:.. Closest calculated PWWP-region atom distance: 2.9309 Å. Five-Å native core contacts: 8; broader-Pfam contacts: 1; 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 | C11 | 4.8037 | 1.0 / 0.97 |
| 232 LYS | native annotation core | C | C11 | 5.5694 | 1.0 / 0.97 |
| 233 ILE | native annotation core | CG1 | C12 | 3.5209 | 1.0 / 0.97 |
| 236 PHE | native annotation core | CG | C10 | 3.7627 | 1.0 / 0.97 |
| 237 SER | native annotation core | O | C11 | 4.7283 | 1.0 / 0.97 |
| 239 TRP | native annotation core | CH2 | C5 | 3.6907 | 1.0 / 0.97 |
| 263 TRP | native annotation core | CH2 | C11 | 3.8086 | 1.0 / 0.97 |
| 265 GLY | native annotation core | C | C8 | 5.5194 | 1.0 / 0.97 |
| 266 ASP | native annotation core | OD2 | C9 | 2.9309 | 1.0 / 0.97 |
| 268 LYS | native annotation core | CD | C9 | 4.5969 | 1.0 / 0.97 |
| 270 SER | native annotation core | OG | C12 | 5.0901 | 1.0 / 0.97 |
| 297 SER | broader pfam outside annotation core | CB | C8 | 4.0262 | 1.0 / 0.97 |
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 / 20 | ILE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 226 / 21 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 227 / 22 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 228 / 23 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 229 / 24 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 230 / 25 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 231 / 26 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 232 / 27 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 233 / 28 | ILE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 234 / 29 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 235 / 30 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 236 / 31 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 237 / 32 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 238 / 33 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 239 / 34 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 240 / 35 | PRO | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 241 / 36 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 242 / 37 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 243 / 38 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 244 / 39 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 245 / 40 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 246 / 41 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 247 / 42 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 248 / 43 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 249 / 44 | THR | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 250 / 45 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 251 / 46 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 252 / 47 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 253 / 48 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 254 / 49 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 255 / 50 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 256 / 51 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 257 / 52 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 258 / 53 | MET | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 259 / 54 | ARG | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 260 / 55 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 261 / 56 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 262 / 57 | GLN | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 263 / 58 | TRP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 264 / 59 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 265 / 60 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 266 / 61 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 267 / 62 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 268 / 63 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 269 / 64 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 270 / 65 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 271 / 66 | GLU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 272 / 67 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 273 / 68 | SER | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 274 / 69 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 275 / 70 | ASP | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 276 / 71 | LYS | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 277 / 72 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 278 / 73 | VAL | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 279 / 74 | ALA | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 280 / 75 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 281 / 76 | GLY | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 282 / 77 | LEU | Yes | — | — | — | —; occupancy ≥ 1.0 |
| 283 / 78 | PHE | Yes | — | — | — | —; occupancy ≥ 1.0 |
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