MolNFT v1 · #181287 · protein
Crystal structure of SARS-cov-2 receptor binding domain in complex with antibodies CV503 and COVA1-16
7LQ7 · Spike protein S1: “Crystal structure of SARS-cov-2 receptor binding domain in complex with antibodies CV503 and COVA1-16”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #181287 on GenesisL1: 3D…
- PDB
- 7LQ7
- Type
- protein
- Length
- 3,216 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; CV503 heavy chain; CV503 light chain; COVA1-16 heavy chain; COVA1-16…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 10 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike protein S1 | protein | 195 | 15% helix, 29% strand | P0DTC2 |
| C | CV503 heavy chain | protein | 224 | 7% helix, 46% strand | — |
| D | CV503 light chain | protein | 214 | 8% helix, 49% strand | — |
| F | CV503 heavy chain | protein | 219 | 7% helix, 47% strand | — |
| G | CV503 light chain | protein | 215 | 8% helix, 49% strand | — |
| L | CV503 light chain | protein | 213 | 8% helix, 48% strand | — |
| T, y | COVA1-16 heavy chain | protein | 226 | 8% helix, 50% strand | — |
| U, Q, z | COVA1-16 light chain | protein | 213 | 6% helix, 51% strand | — |
| P | COVA1-16 heavy chain | protein | 232 | 8% helix, 48% strand | — |
| H | CV503 heavy chain | protein | 223 | 9% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.84 | 0.85 | 116 | empty |
| 2 | 529 | 0.72 | 0.81 | 56 | empty |
| 3 | 983 | 0.70 | 0.74 | 94 | empty |
| 4 | 604 | 0.63 | 0.75 | 66 | empty |
| 5 | 235 | 0.60 | 0.80 | 32 | empty |
Interfaces
34 interfaces between chains.
- C–D · 1826 Ų buried · 13 hydrogen bonds · protein-protein
- P–Q · 1820 Ų buried · 13 hydrogen bonds · protein-protein
- T–U · 1795 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1783 Ų buried · 16 hydrogen bonds · protein-protein
- y–z · 1760 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7LQ7 · Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV503… · 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 7LQ7 · PDBe 7LQ7 · UniProt P0DTC2
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