MolNFT v1 · #169445 · protein
Crystal structure of SARS-cov-2 receptor binding domain in complex with antibodies CC12.3 and CR3022
6XC7 · Spike protein S1: “Crystal structure of SARS-cov-2 receptor binding domain in complex with antibodies CC12.3 and CR3022”. X-ray diffraction, 2 ligands (NAG, BMA), 14 pockets (best druggability 0.66). MolNFT v1 #169445 on GenesisL1…
- PDB
- 6XC7
- Type
- protein
- Length
- 1,065 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; CR3022 heavy chain; CR3022 light chain; CC12.3 heavy chain; CC12.3…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 193 | 17% helix, 29% strand | P0DTC2 |
| H | CR3022 heavy chain | protein | 218 | 7% helix, 50% strand | — |
| L | CR3022 light chain | protein | 221 | 5% helix, 51% strand | — |
| C | CC12.3 heavy chain | protein | 220 | 5% helix, 51% strand | — |
| D | CC12.3 light chain | protein | 213 | 4% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.66 | 0.85 | 26 | empty |
| 2 | 451 | 0.59 | 0.75 | 59 | empty |
| 3 | 331 | 0.57 | 0.76 | 48 | empty |
| 4 | 306 | 0.53 | 0.75 | 45 | empty |
| 5 | 113 | 0.49 | 0.80 | 23 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1896 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1729 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 749 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 622 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 413 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6XC7 · Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.3… · 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 6XC7 · PDBe 6XC7 · UniProt P0DTC2
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