MolNFT v1 · #175731 · protein
S protein of SARS-cov-2 in complex bound with P5A-1B9
7CZX · Spike glycoprotein: “S protein of SARS-cov-2 in complex bound with P5A-1B9”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #175731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CZX
- Type
- protein
- Length
- 4,368 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Immunoglobulin heavy variable 4-59,CHAIN H of P5A-1B9,IGH@ protein…
- UniProt
- P0DTC2, P01825, Q6GMX6, A0A5C2G1U0, Q8TCD0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 31% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 1006 | 19% helix, 30% strand | P0DTC2 |
| H, I, J | Immunoglobulin heavy variable 4-59,CHAIN H of P5A-1B9,IGH@ protein | protein | 230 | 3% helix, 44% strand | P01825, Q6GMX6 |
| K, M, N | Ig C168_LIGHT_IGKV4-1_IGKJ4,UNCHARACTERIZED protein | protein | 220 | 5% helix, 36% strand | A0A5C2G1U0, Q8TCD0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 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 | 1054 | 0.85 | 0.86 | 131 | empty |
| 2 | 1197 | 0.84 | 0.85 | 131 | empty |
| 3 | 619 | 0.82 | 0.87 | 70 | empty |
| 4 | 923 | 0.80 | 0.82 | 76 | empty |
| 5 | 996 | 0.79 | 0.80 | 91 | empty |
Interfaces
13 interfaces between chains.
- A–C · 4462 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4365 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 4164 Ų buried · 27 hydrogen bonds · protein-protein
- H–K · 2026 Ų buried · 10 hydrogen bonds · protein-protein
- I–M · 2017 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 47 glycan (disulfide, N-glycosylation).
Compared structures
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
- Every structure of UniProt P01825
- Every structure of UniProt Q6GMX6
- Every structure of UniProt A0A5C2G1U0
- Every structure of UniProt Q8TCD0
- Elsewhere: RCSB PDB 7CZX · PDBe 7CZX · UniProt P0DTC2 · UniProt P01825 · UniProt Q6GMX6 · UniProt A0A5C2G1U0 · UniProt Q8TCD0
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