Research workbench
S protein of SARS-cov-2 in complex bound with P5A-2G7
Analyse S protein of SARS-cov-2 in complex bound with P5A-2G7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CZW
- Type
- protein
- Length
- 3,880 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Immunoglobulin heavy variable 4-61,CHAIN H of P5A-2G7, epididymis…
- UniProt
- P0DTC2, A0A0C4DH41, V9HW68, A0A5C2G2G8, Q6IPQ0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
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 |
| H, J | Immunoglobulin heavy variable 4-61,CHAIN H of P5A-2G7, epididymis luminal protein 214 | protein | 230 | 4% helix, 45% strand | A0A0C4DH41, V9HW68 |
| L, N | Igl C2312_LIGHT_IGLV2-14_IGLJ2,IGL@ protein | protein | 214 | 5% helix, 41% strand | A0A5C2G2G8, Q6IPQ0 |
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 | 577 | 0.83 | 0.88 | 78 | empty |
| 2 | 654 | 0.82 | 0.86 | 69 | empty |
| 3 | 843 | 0.81 | 0.83 | 69 | empty |
| 4 | 387 | 0.77 | 0.87 | 54 | empty |
| 5 | 259 | 0.76 | 0.89 | 45 | empty |
Interfaces
9 interfaces between chains.
- B–C · 4516 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4252 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 4128 Ų buried · 38 hydrogen bonds · protein-protein
- H–L · 1876 Ų buried · 8 hydrogen bonds · protein-protein
- J–N · 1875 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7CZW · S protein of SARS-CoV-2 in complex bound with P5A-2G7 · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0C4DH41
- Every structure of UniProt V9HW68
- Every structure of UniProt A0A5C2G2G8
- Every structure of UniProt Q6IPQ0
- Elsewhere: RCSB PDB 7CZW · PDBe 7CZW · UniProt P0DTC2 · UniProt A0A0C4DH41 · UniProt V9HW68 · UniProt A0A5C2G2G8 · UniProt Q6IPQ0
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