MolNFT v1 · #190936 · protein
Cryo-EM structure of SARS-cov-2 spike : H11-B5 nanobody complex
7Z85 · Spike GLYCOPROTEIN,FIBRITIN: “Cryo-EM structure of SARS-cov-2 spike : H11-B5 nanobody complex”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #190936 on GenesisL1: 3D structure, binding sites…
- PDB
- 7Z85
- Type
- protein
- Length
- 3,344 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN; Nanobody H11-B5
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 987 | 23% helix, 32% strand | P0DTC2 |
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 992 | 23% helix, 32% strand | P0DTC2 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 990 | 24% helix, 34% strand | P0DTC2 |
| F, D, E | Nanobody H11-B5 | protein | 125 | 6% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 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 | 988 | 0.86 | 0.87 | 115 | empty |
| 2 | 309 | 0.82 | 0.92 | 51 | empty |
| 3 | 964 | 0.81 | 0.83 | 110 | empty |
| 4 | 797 | 0.81 | 0.84 | 70 | empty |
| 5 | 1022 | 0.77 | 0.79 | 91 | empty |
Interfaces
7 interfaces between chains.
- B–C · 5061 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4772 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 4414 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 678 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 666 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7Z85 · CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-B5 nanobody complex · 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 7Z85 · PDBe 7Z85 · UniProt P0DTC2
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