MolNFT v1 · #169459 · protein
Structure of the SARS-cov-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 1)
6XCM: “Structure of the SARS-cov-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment…”. Electron microscopy, 3 ligands (NAG, FUC, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #169459 on GenesisL1: 3D…
- PDB
- 6XCM
- Type
- protein
- Length
- 3,390 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C105 Fab heavy chain; C105 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 21% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 966 | 23% helix, 24% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 985 | 23% helix, 24% strand | P0DTC2 |
| H, N | C105 Fab heavy chain | protein | 116 | 0% helix, 25% strand | — |
| L, S | C105 Fab light chain | protein | 111 | 0% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 55 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B
- BMA · beta-D-mannopyranose · sugar
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 | 817 | 0.86 | 0.88 | 105 | empty |
| 2 | 697 | 0.84 | 0.88 | 82 | empty |
| 3 | 1138 | 0.83 | 0.84 | 114 | empty |
| 4 | 744 | 0.79 | 0.83 | 57 | empty |
| 5 | 491 | 0.74 | 0.83 | 38 | empty |
Interfaces
10 interfaces between chains.
- A–B · 4489 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4317 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 4216 Ų buried · 28 hydrogen bonds · protein-protein
- H–L · 968 Ų buried · 6 hydrogen bonds · protein-protein
- N–S · 902 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 40 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6XCM · Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing… · 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 6XCM · PDBe 6XCM · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.