MolNFT v1 · #177910 · protein
Local cryoem structure of the SARS-cov-2 S6PV2 in complex with bd-771 Fab and bd-821 Fab
7EY5 · Spike glycoprotein: “Local cryoem structure of the SARS-cov-2 S6PV2 in complex with bd-771 Fab and bd-821 Fab”. Electron microscopy, 7 pockets (best druggability 0.67). MolNFT v1 #177910 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7EY5
- Type
- protein
- Length
- 648 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Bd-821H; Bd-821L; Bd-771H; Bd-771L
- UniProt
- P0DTC2
- Pockets
- 7 · best druggability 0.67
Structure
electron microscopy · 5 distinct chains · 5% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 183 | 17% helix, 24% strand | P0DTC2 |
| B | Bd-821H | protein | 120 | 0% helix, 31% strand | — |
| C | Bd-821L | protein | 108 | 0% helix, 37% strand | — |
| H | Bd-771H | protein | 129 | 2% helix, 41% strand | — |
| L | Bd-771L | protein | 108 | 0% helix, 51% strand | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.67 | 0.76 | 67 | empty |
| 2 | 100 | 0.42 | 0.78 | 15 | empty |
| 3 | 60 | 0.39 | 0.80 | 18 | empty |
| 4 | 64 | 0.29 | 0.74 | 19 | empty |
| 5 | 52 | 0.29 | 0.75 | 12 | empty |
Interfaces
7 interfaces between chains.
- B–C · 806 Ų buried · 2 hydrogen bonds · protein-protein
- H–L · 743 Ų buried · 2 hydrogen bonds · protein-protein
- A–H · 638 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 468 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 284 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7EY5 · Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab · 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
- Elsewhere: RCSB PDB 7EY5 · PDBe 7EY5 · UniProt P0DTC2
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