Research workbench
SARS-cov-2 rbd in complex with Fab 15033-7
Analyse SARS-cov-2 rbd in complex with Fab 15033-7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KLH
- Type
- protein
- Length
- 1,269 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 15033-7 heavy chain; Fab 15033-7 light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, I | Fab 15033-7 heavy chain | protein | 223 | 6% helix, 48% strand | — |
| L, M | Fab 15033-7 light chain | protein | 214 | 7% helix, 50% strand | — |
| B | Spike glycoprotein | protein | 195 | 15% helix, 28% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 200 | 15% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, B, M, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.69 | 0.78 | 59 | NAG |
| 2 | 339 | 0.69 | 0.82 | 28 | empty |
| 3 | 399 | 0.68 | 0.81 | 33 | empty |
| 4 | 529 | 0.66 | 0.77 | 47 | NAG |
| 5 | 50 | 0.66 | 0.95 | 19 | empty |
Interfaces
9 interfaces between chains.
- I–M · 1991 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1982 Ų buried · 17 hydrogen bonds · protein-protein
- M–B · 688 Ų buried · 10 hydrogen bonds · protein-protein
- L–A · 680 Ų buried · 11 hydrogen bonds · protein-protein
- H–A · 451 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KLH · SARS-CoV-2 RBD in complex with Fab 15033-7 · the same entry in another collection · chain H against H, 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 7KLH · PDBe 7KLH · UniProt P0DTC2
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