MolNFT v1 · #175723 · protein
S protein of SARS-cov-2 in complex bound with P2B-1A1
7CZP · Spike glycoprotein: “S protein of SARS-cov-2 in complex bound with P2B-1A1”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #175723 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CZP
- Type
- protein
- Length
- 3,862 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Immunoglobulin heavy variable 4-59,CHAIN H of P2B-1A1,ANTI- rhd…
- UniProt
- P0DTC2, P01825, Q5EFE5, A0A5C2GM57, Q8N5F4
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 982 | 19% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1004 | 21% helix, 31% strand | P0DTC2 |
| H, J | Immunoglobulin heavy variable 4-59,CHAIN H of P2B-1A1,ANTI- rhd monoclonal T125 GAMMA1 heavy chain | protein | 222 | 3% helix, 35% strand | P01825, Q5EFE5 |
| L, N | Ig C181_LIGHT_IGLV2-14_IGLJ3,IGL@ protein | protein | 213 | 5% helix, 43% strand | A0A5C2GM57, Q8N5F4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 74 copies · chains A, B, C, H, L, J, N
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 | 1044 | 0.85 | 0.86 | 127 | empty |
| 2 | 654 | 0.83 | 0.87 | 68 | empty |
| 3 | 588 | 0.80 | 0.85 | 69 | empty |
| 4 | 1052 | 0.79 | 0.81 | 88 | empty |
| 5 | 657 | 0.79 | 0.84 | 87 | empty |
Interfaces
10 interfaces between chains.
- B–C · 4492 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4260 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 4184 Ų buried · 38 hydrogen bonds · protein-protein
- H–L · 1745 Ų buried · 5 hydrogen bonds · protein-protein
- J–N · 1740 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 glycan, 46 disulfide (N-glycosylation, disulfide).
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 Q5EFE5
- Every structure of UniProt A0A5C2GM57
- Every structure of UniProt Q8N5F4
- Elsewhere: RCSB PDB 7CZP · PDBe 7CZP · UniProt P0DTC2 · UniProt P01825 · UniProt Q5EFE5 · UniProt A0A5C2GM57 · UniProt Q8N5F4
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