MolNFT v1 · #181097 · protein
Crystal structure of SARS-cov-2 rbd-targeting antibody COV107-23
7LKA · COV107-23 heavy chain: “Crystal structure of SARS-cov-2 rbd-targeting antibody COV107-23”. X-ray diffraction, 12 pockets (best druggability 0.81). MolNFT v1 #181097 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LKA
- Type
- protein
- Length
- 1,718 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COV107-23 heavy chain; COV107-23 light chain
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | COV107-23 heavy chain | protein | 216 | 7% helix, 53% strand | — |
| L, B | COV107-23 light chain | protein | 213 | 7% helix, 51% strand | — |
| A | COV107-23 heavy chain | protein | 211 | 6% helix, 53% strand | — |
| C | COV107-23 heavy chain | protein | 219 | 7% helix, 52% strand | — |
| D | COV107-23 light chain | protein | 215 | 6% helix, 52% strand | — |
| E | COV107-23 heavy chain | protein | 217 | 4% helix, 53% strand | — |
| F | COV107-23 light chain | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.81 | 0.82 | 132 | empty |
| 2 | 305 | 0.65 | 0.81 | 40 | empty |
| 3 | 464 | 0.63 | 0.77 | 48 | empty |
| 4 | 273 | 0.59 | 0.78 | 37 | empty |
| 5 | 310 | 0.53 | 0.74 | 40 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1867 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1858 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1854 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1759 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 626 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 7LKA · Crystal structure of SARS-CoV-2 RBD-targeting antibody COV107-23 · 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
- Elsewhere: RCSB PDB 7LKA · PDBe 7LKA
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