MolNFT v1 · #190743 · protein
SARS-cov-2 spike (6P) in complex with 1 R1-32 Fab
7YDY · Spike glycoprotein: “SARS-cov-2 spike (6P) in complex with 1 R1-32 Fab”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #190743 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7YDY
- Type
- protein
- Length
- 3,638 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of R1-32 Fab; Light chain of R1-32 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 12% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1066 | 16% helix, 27% strand | P0DTC2 |
| H | Heavy chain of R1-32 Fab | protein | 227 | 1% helix, 43% strand | — |
| L | Light chain of R1-32 Fab | protein | 213 | 3% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 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 | 1018 | 0.86 | 0.87 | 131 | empty |
| 2 | 339 | 0.85 | 0.94 | 50 | empty |
| 3 | 285 | 0.84 | 0.94 | 29 | empty |
| 4 | 1063 | 0.82 | 0.83 | 97 | empty |
| 5 | 1082 | 0.78 | 0.80 | 90 | empty |
Interfaces
7 interfaces between chains.
- A–C · 5632 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 5382 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 4568 Ų buried · 42 hydrogen bonds · protein-protein
- H–L · 1909 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 897 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7YDY · SARS-CoV-2 Spike (6P) in complex with 1 R1-32 Fab · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 7YDY · PDBe 7YDY · UniProt P0DTC2
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