Research workbench
Local resolution of BD55-5840 Fab and SARS-COV2 omicron rbd
Analyse Local resolution of BD55-5840 Fab and SARS-COV2 omicron rbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WRZ
- Type
- protein
- Length
- 414 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BD55-5840H; BD55-5840L; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.60
Structure
electron microscopy · 3 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | BD55-5840H | protein | 119 | 0% helix, 48% strand | — |
| L | BD55-5840L | protein | 109 | 3% helix, 47% strand | — |
| R | Spike protein S1 | protein | 186 | 19% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, R, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.60 | 0.76 | 53 | NAG |
| 2 | 71 | 0.34 | 0.76 | 13 | empty |
| 3 | 61 | 0.33 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 769 Ų buried · 4 hydrogen bonds · protein-protein
- H–R · 502 Ų buried · 5 hydrogen bonds · protein-protein
- L–R · 466 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WRZ · Local resolution of BD55-5840 Fab and SARS-COV2 Omicron RBD · 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 7WRZ · PDBe 7WRZ · UniProt P0DTC2
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