Research workbench
Crystallographic structure of neutralizing antibody 2-15 in complex with SARS-cov-2 spike receptor-binding domain (rbd).
Analyse Crystallographic structure of neutralizing antibody 2-15 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L5B
- Type
- protein
- Length
- 599 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; 2-15 heavy chain; 2-15 light chain
- UniProt
- P0DTC2
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 170 | 9% helix, 19% strand | P0DTC2 |
| H | 2-15 heavy chain | protein | 218 | 4% helix, 45% strand | — |
| L | 2-15 light chain | protein | 211 | 6% helix, 45% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.71 | 0.92 | 24 | empty |
| 2 | 227 | 0.61 | 0.81 | 23 | empty |
| 3 | 319 | 0.51 | 0.73 | 39 | empty |
| 4 | 90 | 0.37 | 0.76 | 17 | empty |
| 5 | 72 | 0.32 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1680 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 760 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 207 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7L5B · Crystallographic structure of neutralizing antibody 2-15 in complex with SARS-CoV-2 spike… · 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 7L5B · PDBe 7L5B · UniProt P0DTC2
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