9C6Y
Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, C (A, C) | Heavy chain of COV2-3906 Fab | polymer | 225 | 23972.9 | 2 | Homo sapiens (human) | ||
| 2 | B, D (B, D) | Light chain of COV2-3906 Fab | polymer | 216 | 23098.3 | 2 | Homo sapiens (human) | ||
| 3 | E, F (E, F) | Spike protein S2' | polymer | 216 | 24446.7 | 2 | UniProt (P0DTC2) Pfam (PF09408) | Severe acute respiratory syndrome coronavirus | |
| 4 | G (G) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 732.7 | 1 | In PDB GlyTouCan (G32152BH) | |||
| 5 | H (H) | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 894.8 | 1 | In PDB GlyTouCan (G00395TQ) | |||
| 6 | I, J, O, P, S (B, E, F) | SULFATE ION | non-polymer | 96.1 | 5 | Chemie (SO4) | |||
| 7 | K, L (B, D) | CHLORIDE ION | non-polymer | 35.5 | 2 | Chemie (CL) | |||
| 8 | M, Q (E, F) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 2 | Chemie (NAG) | |||
| 9 | N, R (E, F) | 2-acetamido-2-deoxy-alpha-D-galactopyranose | non-polymer | 221.2 | 2 | Chemie (A2G) | |||
| 10 | T, U, V, W, X... (A, B, C, D, E...) | water | water | 18.0 | 94 | Chemie (HOH) |
Sequence modifications
E, F: 319 - 534 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| His 339 | Gly 339 | conflict |
| Thr 346 | Arg 346 | conflict |
| Phe 365 | Tyr 365 | conflict |
| Ile 368 | Leu 368 | conflict |
| Phe 371 | Ser 371 | conflict |
| Pro 373 | Ser 373 | conflict |
| Phe 375 | Ser 375 | conflict |
| Ala 376 | Thr 376 | conflict |
| Trp 392 | Phe 392 | conflict |
| Ile 395 | Val 395 | conflict |
| Asn 405 | Asp 405 | conflict |
| Ser 408 | Arg 408 | conflict |
| Asn 417 | Lys 417 | conflict |
| Lys 440 | Asn 440 | conflict |
| Pro 445 | Val 445 | conflict |
| Ser 446 | Gly 446 | conflict |
| Lys 460 | Asn 460 | conflict |
| Asn 477 | Ser 477 | conflict |
| Lys 478 | Thr 478 | conflict |
| Ala 484 | Glu 484 | conflict |
| Pro 486 | Phe 486 | conflict |
| Ser 490 | Phe 490 | conflict |
| Arg 498 | Gln 498 | conflict |
| Tyr 501 | Asn 501 | conflict |
| His 505 | Tyr 505 | conflict |
| Leu 529 | Lys 529 | conflict |
| Glu 530 | Ser 530 | conflict |
| Val 531 | Thr 531 | conflict |
| Leu 532 | Asn 532 | conflict |
| Phe 533 | Leu 533 | conflict |
| Gln 534 | Val 534 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 143035.8 | |
| Branched | Number of molecules | 2 |
| Total formula weight | 1627.5 | |
| Non-Polymers* | Number of molecules | 11 |
| Total formula weight | 1436.1 | |
| All* | Total formula weight | 146099.4 |
