MolNFT v1 · #190465 · protein
SARS-cov-2 spike rbd in complex with neutralizing antibody UT28K
7X7O · Spike protein S1: “SARS-cov-2 spike rbd in complex with neutralizing antibody UT28K”. X-ray diffraction, 15 pockets (best druggability 0.69). MolNFT v1 #190465 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7X7O
- Type
- protein
- Length
- 1,575 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; UT28K Fab, heavy chain; UT28K Fab, light chain
- UniProt
- P0DTC2
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 167 | 10% helix, 25% strand | P0DTC2 |
| B | Spike protein S1 | protein | 172 | 9% helix, 26% strand | P0DTC2 |
| C | Spike protein S1 | protein | 157 | 7% helix, 25% strand | P0DTC2 |
| D | Spike protein S1 | protein | 163 | 10% helix, 23% strand | P0DTC2 |
| E, G, H, J | UT28K Fab, heavy chain | protein | 122 | 2% helix, 48% strand | — |
| F, I, K, L | UT28K Fab, light chain | protein | 107 | 6% helix, 44% strand | — |
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.69 | 0.78 | 61 | empty |
| 2 | 537 | 0.68 | 0.78 | 65 | empty |
| 3 | 537 | 0.65 | 0.76 | 47 | empty |
| 4 | 643 | 0.64 | 0.74 | 62 | empty |
| 5 | 121 | 0.49 | 0.80 | 19 | empty |
Interfaces
21 interfaces between chains.
- G–I · 851 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 839 Ų buried · 7 hydrogen bonds · protein-protein
- H–L · 821 Ų buried · 9 hydrogen bonds · protein-protein
- J–K · 812 Ų buried · 8 hydrogen bonds · protein-protein
- B–H · 604 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 7X7O · SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K · 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 7X7O · PDBe 7X7O · UniProt P0DTC2
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