Research workbench
S protein of SARS-cov-2 in complex bound with P5A-1B6_3B
Analyse S protein of SARS-cov-2 in complex bound with P5A-1B6_3B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CZV
- Type
- protein
- Length
- 4,346 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Immunoglobulin heavy variable 3-30-3,CHAIN H of P5A-1B6_3B…
- UniProt
- P0DTC2, P0DP02, P0DOX5, P01594, Q8TCD0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1007 | 20% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1004 | 21% helix, 29% strand | P0DTC2 |
| H, I, J | Immunoglobulin heavy variable 3-30-3,CHAIN H of P5A-1B6_3B, immunoglobulin gamma-1 heavy chain | protein | 229 | 3% helix, 41% strand | P0DP02, P0DOX5 |
| K, M, N | Immunoglobulin kappa variable 1-33,UNCHARACTERIZED protein | protein | 214 | 5% helix, 35% strand | P01594, Q8TCD0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.82 | 0.87 | 67 | empty |
| 2 | 408 | 0.79 | 0.88 | 59 | empty |
| 3 | 409 | 0.79 | 0.87 | 69 | empty |
| 4 | 418 | 0.78 | 0.87 | 69 | empty |
| 5 | 413 | 0.77 | 0.86 | 74 | empty |
Interfaces
14 interfaces between chains.
- B–C · 4258 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 4167 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 4134 Ų buried · 39 hydrogen bonds · protein-protein
- H–K · 1853 Ų buried · 7 hydrogen bonds · protein-protein
- I–M · 1844 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7CZV · S protein of SARS-CoV-2 in complex bound with P5A-1B6_3B · the same entry in another collection · chain N against N, TM-score 1.00
- P01594 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa variable 1-33 (P01594) · a predicted model of the same protein · chain K against A, TM-score 0.42
- P0DP02 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy variable 3-30-3 (P0DP02) · a predicted model of the same protein · chain H against A, TM-score 0.42
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTC2
- Every structure of UniProt P0DP02
- Every structure of UniProt P0DOX5
- Every structure of UniProt P01594
- Every structure of UniProt Q8TCD0
- Elsewhere: RCSB PDB 7CZV · PDBe 7CZV · UniProt P0DTC2 · UniProt P0DP02 · UniProt P0DOX5 · UniProt P01594 · UniProt Q8TCD0
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