Research workbench
S protein of SARS-cov-2 in complex bound with P5A-1B6_2B
Analyse S protein of SARS-cov-2 in complex bound with P5A-1B6_2B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CZU
- Type
- protein
- Length
- 3,878 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Immunoglobulin heavy variable 3-30-3,IMMUNOGLOBULIN heavy variable…
- UniProt
- P0DTC2, P0DP02, P0DOX5, P01594, Q8TCD0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 982 | 19% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1004 | 21% helix, 31% strand | P0DTC2 |
| J, H | Immunoglobulin heavy variable 3-30-3,IMMUNOGLOBULIN heavy variable 3-30-3,CHAIN H of P5A-1B6_2B,IMMUNOGLOBULIN gamma-1 heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy chain | protein | 229 | 3% helix, 41% strand | P0DP02, P0DOX5 |
| N, K | Immunoglobulin kappa variable 1-33,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 · 70 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 | 1062 | 0.85 | 0.86 | 130 | empty |
| 2 | 793 | 0.80 | 0.84 | 90 | empty |
| 3 | 1018 | 0.80 | 0.81 | 85 | empty |
| 4 | 668 | 0.79 | 0.84 | 85 | empty |
| 5 | 355 | 0.75 | 0.86 | 57 | empty |
Interfaces
10 interfaces between chains.
- B–C · 4602 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4227 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 4057 Ų buried · 38 hydrogen bonds · protein-protein
- J–N · 1853 Ų buried · 7 hydrogen bonds · protein-protein
- H–K · 1852 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 44 disulfide (N-glycosylation, disulfide).
Compared structures
- 7CZU · S protein of SARS-CoV-2 in complex bound with P5A-1B6_2B · the same entry in another collection · chain K against K, 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 N 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 J 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 7CZU · PDBe 7CZU · UniProt P0DTC2 · UniProt P0DP02 · UniProt P0DOX5 · UniProt P01594 · UniProt Q8TCD0
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