MolNFT v1 · #177126 · protein
SARS-cov-2 S-6P in complex with 9 fabs
7E8C · Spike glycoprotein: “SARS-cov-2 S-6P in complex with 9 fabs”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #177126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E8C
- Type
- protein
- Length
- 5,218 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 604 H; 604 L; N9 H; 368-2 L; 368-2 H; N9 L
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1052 | 20% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1054 | 21% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1051 | 21% helix, 31% strand | P0DTC2 |
| D, N, O | 604 H | protein | 116 | 5% helix, 49% strand | — |
| E, P, Q | 604 L | protein | 106 | 0% helix, 46% strand | — |
| H, S, T | N9 H | protein | 124 | 11% helix, 43% strand | — |
| I, J, Z | 368-2 L | protein | 112 | 0% helix, 45% strand | — |
| K, M, a | 368-2 H | protein | 124 | 5% helix, 49% strand | — |
| L, U, V | N9 L | protein | 105 | 6% helix, 50% strand | — |
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 | 1165 | 0.83 | 0.84 | 114 | empty |
| 2 | 552 | 0.81 | 0.87 | 58 | empty |
| 3 | 890 | 0.79 | 0.82 | 88 | empty |
| 4 | 900 | 0.79 | 0.81 | 77 | empty |
| 5 | 1105 | 0.77 | 0.79 | 110 | empty |
Interfaces
42 interfaces between chains.
- B–C · 4350 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 4214 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 4153 Ų buried · 32 hydrogen bonds · protein-protein
- Z–a · 939 Ų buried · 10 hydrogen bonds · protein-protein
- I–K · 925 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide (disulfide).
Compared structures
- 7E8C · SARS-CoV-2 S-6P in complex with 9 Fabs · 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 7E8C · PDBe 7E8C · UniProt P0DTC2
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