MolNFT v1 · #177953 · protein
Local cryoem structure of the SARS-cov-2 S6PV2 in complex with bd-812 Fab and bd-836 Fab
7EZV · Spike glycoprotein: “Local cryoem structure of the SARS-cov-2 S6PV2 in complex with bd-812 Fab and bd-836 Fab”. Electron microscopy, 5 pockets (best druggability 0.43). MolNFT v1 #177953 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7EZV
- Type
- protein
- Length
- 632 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 812 H; 812L; 836H; 836L
- UniProt
- P0DTC2
- Pockets
- 5 · best druggability 0.43
Structure
electron microscopy · 5 distinct chains · 6% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 183 | 14% helix, 25% strand | P0DTC2 |
| H | 812 H | protein | 116 | 3% helix, 46% strand | — |
| L | 812L | protein | 106 | 3% helix, 42% strand | — |
| M | 836H | protein | 120 | 8% helix, 44% strand | — |
| N | 836L | protein | 107 | 0% helix, 40% strand | — |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.43 | 0.80 | 18 | empty |
| 2 | 154 | 0.42 | 0.74 | 22 | empty |
| 3 | 94 | 0.36 | 0.75 | 19 | empty |
| 4 | 69 | 0.30 | 0.74 | 18 | empty |
| 5 | 63 | 0.27 | 0.72 | 14 | empty |
Interfaces
6 interfaces between chains.
- M–N · 860 Ų buried · 6 hydrogen bonds · protein-protein
- H–L · 731 Ų buried · 6 hydrogen bonds · protein-protein
- A–M · 618 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 600 Ų buried · 7 hydrogen bonds · protein-protein
- A–N · 271 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7EZV · local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-812 Fab and BD-836 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 7EZV · PDBe 7EZV · UniProt P0DTC2
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