11ZW
Structure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | PDCoV IL121_2014 receptor binding domain | polymer | 175 | 19285.9 | 1 | UniProt (F1NWE3) UniProt (W8Q9Y7) | Porcine deltacoronavirus | R-PTP-S,Chick receptor tyrosine phosphatase alpha,CRYP alpha,CRYPalpha |
| 2 | B (B) | RBD minibinder 11 | polymer | 176 | 20905.8 | 1 | synthetic construct | ||
| 3 | C (H) | PD3 Fab fragment heavy chain | polymer | 261 | 27880.5 | 1 | Mus musculus (mouse) | ||
| 4 | D (L) | PD3 Fab fragment light chain | polymer | 238 | 25967.2 | 1 | Mus musculus (mouse) | ||
| 5 | E (N) | Kappa light chain nanobody | polymer | 159 | 17252.1 | 1 | Lama glama (llama) | ||
| 6 | F (C) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 910.8 | 1 | In PDB | |||
| 7 | G (D) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB | |||
| 8 | H, I, J, K, L (A, B, H, L, N) | water | water | 18.0 | 216 | Chemie (HOH) |
Sequence modifications
A: 271 - 302 (UniProt: F1NWE3)
A: 303 - 416 (UniProt: W8Q9Y7)
| PDB | External Database | Details |
|---|---|---|
| Gly 272 | Arg 2 | conflict |
| Thr 300 | Ser 30 | conflict |
| Gly 301 | Pro 31 | conflict |
| Thr 302 | Pro 32 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Gly 417 | - | linker |
| Gly 418 | - | linker |
| Ser 419 | - | linker |
| Gly 420 | - | insertion |
| Leu 421 | - | insertion |
| Asn 422 | - | insertion |
| Asp 423 | - | insertion |
| Ile 424 | - | insertion |
| Phe 425 | - | insertion |
| Glu 426 | - | insertion |
| Ala 427 | - | insertion |
| Gln 428 | - | insertion |
| Lys 429 | - | insertion |
| Ile 430 | - | insertion |
| Glu 431 | - | insertion |
| Trp 432 | - | insertion |
| His 433 | - | insertion |
| Glu 434 | - | insertion |
| Gly 435 | - | linker |
| Gly 436 | - | linker |
| Ser 437 | - | linker |
| His 438 | - | expression tag |
| His 439 | - | expression tag |
| His 440 | - | expression tag |
| His 441 | - | expression tag |
| His 442 | - | expression tag |
| His 443 | - | expression tag |
| His 444 | - | expression tag |
| His 445 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 5 |
| Total formula weight | 111291.5 | |
| Branched | Number of molecules | 2 |
| Total formula weight | 1335.2 | |
| All* | Total formula weight | 112626.7 |
