8EPP
Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs in the open conformation
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B, C | Spike glycoprotein | polymer | 1121 | 123913.3 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | D, H, J, K, L... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 9 | In PDB GlyTouCan (G42666HT) | |||
| 3 | E, F, M | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 3 | In PDB GlyTouCan (G15407YE) | |||
| 4 | G, I, O | 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 | 3 | In PDB GlyTouCan (G22768VO) | |||
| 5 | B, C, A | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 24 | Chemie (NAG) |
Sequence modifications
A, B, C: 27 - 1147 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Gly 614 | Asp 614 | conflict |
| Gly 682 | Arg 682 | conflict |
| Ser 683 | Arg 683 | conflict |
| Ser 685 | Arg 685 | conflict |
| Glu 701 | Ala 701 | conflict |
| Ile 727 | Leu 727 | conflict |
| Gln 732 | Thr 732 | conflict |
| Val 734 | Thr 734 | conflict |
| Glu 747 | Thr 747 | conflict |
| His 768 | Thr 768 | conflict |
| Glu 769 | Gly 769 | conflict |
| Ala 817 | Phe 817 | conflict |
| Gly 836 | Gln 836 | conflict |
| Ala 872 | Gln 872 | conflict |
| Ala 884 | Ser 884 | conflict |
| Lys 929 | Ser 929 | conflict |
| Gly 937 | Ser 937 | conflict |
| Pro 986 | Lys 986 | conflict |
| Pro 987 | Val 987 | conflict |
| Asn 998 | Thr 998 | conflict |
| Ala 1003 | Ser 1003 | conflict |
| Asn 1005 | Gln 1005 | conflict |
| Glu 1027 | Thr 1027 | conflict |
| Thr 1070 | Ala 1070 | conflict |
| Tyr 1072 | Glu 1072 | conflict |
| Asn 1084 | Asp 1084 | conflict |
| Asp 1125 | Asn 1125 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 3 |
| Total formula weight | 371739.8 | |
| Branched | Number of molecules | 15 |
| Total formula weight | 8311.7 | |
| Non-Polymers* | Number of molecules | 24 |
| Total formula weight | 5309.0 | |
| All* | Total formula weight | 385360.5 |
