MolNFT v1 · #175746 · protein
S protein of SARS-cov-2 in complex bound with P5A-3C12_2B
7D0D · Spike glycoprotein: “S protein of SARS-cov-2 in complex bound with P5A-3C12_2B”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #175746 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7D0D
- Type
- protein
- Length
- 3,468 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of P5A-3C12; Light chain of P5A-3C12
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1004 | 21% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 982 | 19% helix, 31% strand | P0DTC2 |
| H, G | Heavy chain of P5A-3C12 | protein | 125 | 5% helix, 41% strand | — |
| L, F | Light chain of P5A-3C12 | protein | 113 | 0% helix, 32% strand | — |
| B | Spike glycoprotein | protein | 1006 | 21% helix, 33% strand | P0DTC2 |
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 | 947 | 0.86 | 0.87 | 126 | empty |
| 2 | 1016 | 0.82 | 0.83 | 91 | empty |
| 3 | 815 | 0.80 | 0.83 | 91 | empty |
| 4 | 431 | 0.80 | 0.88 | 65 | empty |
| 5 | 627 | 0.73 | 0.80 | 59 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4538 Ų buried · 33 hydrogen bonds · protein-protein
- C–B · 4183 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 4116 Ų buried · 38 hydrogen bonds · protein-protein
- H–L · 1049 Ų buried · 17 hydrogen bonds · protein-protein
- G–F · 1045 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 7D0D · S protein of SARS-CoV-2 in complex bound with P5A-3C12_2B · 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 7D0D · PDBe 7D0D · UniProt P0DTC2
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