MolNFT v1 · #186373 · protein
SARS-cov-2 spike in complex with PVI.V6-14 Fab
7RBV · PVI.V6-14 Fab light chain, variable region: “SARS-cov-2 spike in complex with PVI.V6-14 Fab”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.88). MolNFT v1 #186373 on GenesisL1: 3D structure, binding…
- PDB
- 7RBV
- Type
- protein
- Length
- 3,718 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PVI.V6-14 Fab light chain, variable region; PVI.V6-14 Fab heavy chain, variable region…
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 15% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| l, L | PVI.V6-14 Fab light chain, variable region | protein | 107 | 0% helix, 34% strand | — |
| h, H | PVI.V6-14 Fab heavy chain, variable region | protein | 126 | 0% helix, 41% strand | — |
| A, B, C | Spike glycoprotein | protein | 1084 | 19% helix, 26% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains B, C, A
- BMA · beta-D-mannopyranose · sugar · 15 copies
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 | 1015 | 0.88 | 0.89 | 127 | empty |
| 2 | 1081 | 0.85 | 0.85 | 103 | empty |
| 3 | 1014 | 0.82 | 0.84 | 90 | empty |
| 4 | 1016 | 0.80 | 0.81 | 88 | empty |
| 5 | 852 | 0.80 | 0.82 | 68 | empty |
Interfaces
11 interfaces between chains.
- A–C · 4564 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 4480 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4302 Ų buried · 32 hydrogen bonds · protein-protein
- l–h · 867 Ų buried · 2 hydrogen bonds · protein-protein
- L–H · 818 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 43 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RBV · SARS-CoV-2 Spike in complex with PVI.V6-14 Fab · the same entry in another collection · chain l against l, 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 7RBV · PDBe 7RBV · UniProt P0DTC2
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