8HC7
SARS-CoV-2 Omicron BA.1 spike trimer (6P) complex with YB9-258 Fab, focused refinement of RBD-dimer region
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | C | Spike protein S1 | polymer | 510 | 58054.4 | 1 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) In PDB | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | |
2 | A | Spike protein S1 | polymer | 267 | 30244.2 | 1 | UniProt (P0DTC2) Pfam (PF09408) Pfam (PF19209) In PDB | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | |
3 | H | Heavy chain variable region of YB9-258 | polymer | 115 | 12356.8 | 1 | Homo sapiens | ||
4 | L | Light chain variable region of YB9-258 | polymer | 107 | 11288.6 | 1 | Homo sapiens | ||
5 | C, A | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 7 | Chemie (NAG) |
Sequence modifications
C: 14 - 526 (UniProt: P0DTC2)
A: 322 - 588 (UniProt: P0DTC2)
PDB | External Database | Details |
---|---|---|
Val 67 | Ala 67 | variant |
- | His 69 | deletion |
- | Val 70 | deletion |
Ile 95 | Thr 95 | variant |
- | Gly 142 | deletion |
- | Val 143 | deletion |
- | Tyr 144 | deletion |
Asp 142 | Tyr 145 | variant |
Ile 210 | - | insertion |
Val 210 | - | insertion |
Arg 210 | Asn 211 | variant |
Glu 210 | Leu 212 | variant |
Pro 210 | Val 213 | variant |
Glu 210 | Arg 214 | variant |
Asp 339 | Gly 339 | variant |
Leu 371 | Ser 371 | variant |
Pro 373 | Ser 373 | variant |
Phe 375 | Ser 375 | variant |
Asn 417 | Lys 417 | variant |
Lys 440 | Asn 440 | variant |
Ser 446 | Gly 446 | variant |
Asn 477 | Ser 477 | variant |
Lys 478 | Thr 478 | variant |
Ala 484 | Glu 484 | variant |
Arg 493 | Gln 493 | variant |
Ser 496 | Gly 496 | variant |
Arg 498 | Gln 498 | variant |
Tyr 501 | Asn 501 | variant |
His 505 | Tyr 505 | variant |
PDB | External Database | Details |
---|---|---|
Asp 339 | Gly 339 | variant |
Leu 371 | Ser 371 | variant |
Pro 373 | Ser 373 | variant |
Phe 375 | Ser 375 | variant |
Asn 417 | Lys 417 | variant |
Lys 440 | Asn 440 | variant |
Ser 446 | Gly 446 | variant |
Asn 477 | Ser 477 | variant |
Lys 478 | Thr 478 | variant |
Ala 484 | Glu 484 | variant |
Arg 493 | Gln 493 | variant |
Ser 496 | Gly 496 | variant |
Arg 498 | Gln 498 | variant |
Tyr 501 | Asn 501 | variant |
His 505 | Tyr 505 | variant |
Lys 547 | Thr 547 | variant |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 4 |
Total formula weight | 111944.0 | |
Non-Polymers* | Number of molecules | 7 |
Total formula weight | 1548.5 | |
All* | Total formula weight | 113492.4 |