MolNFT v1 · #175725 · protein
S protein of SARS-cov-2 in complex bound with P5A-1B8_2B
7CZR · Spike glycoprotein: “S protein of SARS-cov-2 in complex bound with P5A-1B8_2B”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #175725 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7CZR
- Type
- protein
- Length
- 3,854 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Ig C542_HEAVY_IGHV3-53_IGHD3-10_IGHJ6,IGH@ protein; Igl…
- UniProt
- P0DTC2, A0A5C2GG81, Q6GMX6, A0A5C2GCZ2, Q8TCD0
- 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 | Ig C542_HEAVY_IGHV3-53_IGHD3-10_IGHJ6,IGH@ protein | protein | 217 | 4% helix, 44% strand | A0A5C2GG81, Q6GMX6 |
| K, N | Igl C4203_LIGHT_IGKV1-9_IGKJ4,IGL C4203_LIGHT_IGKV1- 9_IGKJ4,UNCHARACTERIZED protein | protein | 214 | 5% helix, 38% strand | A0A5C2GCZ2, Q8TCD0 |
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 | 1016 | 0.85 | 0.86 | 116 | empty |
| 2 | 578 | 0.83 | 0.88 | 87 | empty |
| 3 | 618 | 0.82 | 0.87 | 68 | empty |
| 4 | 959 | 0.80 | 0.82 | 82 | empty |
| 5 | 440 | 0.76 | 0.85 | 52 | empty |
Interfaces
11 interfaces between chains.
- B–C · 4494 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4231 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 4156 Ų buried · 39 hydrogen bonds · protein-protein
- J–N · 1798 Ų buried · 8 hydrogen bonds · protein-protein
- H–K · 1797 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 46 disulfide (N-glycosylation, disulfide).
Compared structures
- 7CZR · S protein of SARS-CoV-2 in complex bound with P5A-1B8_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
- Every structure of UniProt A0A5C2GG81
- Every structure of UniProt Q6GMX6
- Every structure of UniProt A0A5C2GCZ2
- Every structure of UniProt Q8TCD0
- Elsewhere: RCSB PDB 7CZR · PDBe 7CZR · UniProt P0DTC2 · UniProt A0A5C2GG81 · UniProt Q6GMX6 · UniProt A0A5C2GCZ2 · UniProt Q8TCD0
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