MolNFT v1 · #175624 · protein
P17-H014 Fab cocktail in complex with SARS-cov-2 spike protein
7CWN · Spike glycoprotein: “P17-H014 Fab cocktail in complex with SARS-cov-2 spike protein”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.89). MolNFT v1 #175624 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7CWN
- Type
- protein
- Length
- 4,583 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of P17 Fab; Light chain of P17 Fab; Light chain of H014…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 7 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1072 | 21% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1070 | 22% helix, 30% strand | P0DTC2 |
| K, L, G | Heavy chain of P17 Fab | protein | 120 | 5% helix, 45% strand | — |
| I | Light chain of P17 Fab | protein | 108 | 0% helix, 54% strand | — |
| D, N, M | Light chain of H014 Fab | protein | 107 | 0% helix, 46% strand | — |
| E, H, O | Heavy chain of H014 Fab | protein | 122 | 2% helix, 45% strand | — |
| J, F | Light chain of P17 Fab | protein | 107 | 0% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 46 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 | 837 | 0.89 | 0.91 | 118 | empty |
| 2 | 528 | 0.75 | 0.83 | 38 | empty |
| 3 | 743 | 0.73 | 0.79 | 83 | empty |
| 4 | 560 | 0.73 | 0.81 | 42 | empty |
| 5 | 598 | 0.73 | 0.80 | 37 | empty |
Interfaces
21 interfaces between chains.
- A–C · 4207 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4183 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4169 Ų buried · 40 hydrogen bonds · protein-protein
- G–F · 878 Ų buried · 8 hydrogen bonds · protein-protein
- L–J · 872 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7CWN · P17-H014 Fab cocktail in complex with SARS-CoV-2 spike protein · 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 7CWN · PDBe 7CWN · UniProt P0DTC2
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