MolNFT v1 · #179410 · protein
SARS-cov-2 spike in complex with the S2E12 neutralizing antibody Fab fragment
7K4N · Spike glycoprotein: “SARS-cov-2 spike in complex with the S2E12 neutralizing antibody Fab fragment”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #179410 on GenesisL1: 3D structure, binding…
- PDB
- 7K4N
- Type
- protein
- Length
- 3,654 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2E12 neutralizing antibody Fab fragment (heavy chain); S2E12…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 998 | 22% helix, 35% strand | P0DTC2 |
| H, C, F | S2E12 neutralizing antibody Fab fragment (heavy chain) | protein | 120 | 10% helix, 51% strand | — |
| L, D, G | S2E12 neutralizing antibody Fab fragment (light chain) | protein | 100 | 6% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, B, E
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 | 719 | 0.84 | 0.88 | 103 | empty |
| 2 | 984 | 0.82 | 0.83 | 113 | empty |
| 3 | 1059 | 0.81 | 0.83 | 115 | empty |
| 4 | 1065 | 0.81 | 0.82 | 120 | empty |
| 5 | 1099 | 0.80 | 0.82 | 117 | empty |
Interfaces
12 interfaces between chains.
- A–E · 4157 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 4153 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4121 Ų buried · 34 hydrogen bonds · protein-protein
- F–G · 344 Ų buried · 0 hydrogen bonds · protein-protein
- H–L · 344 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7K4N · SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment · 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 7K4N · PDBe 7K4N · UniProt P0DTC2
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