Research workbench
SARS-cov-2 omicron rbd in complex with nanobody C1, omi-18 and omi-31 fabs
Analyse SARS-cov-2 omicron rbd in complex with nanobody C1, omi-18 and omi-31 fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZFB
- Type
- protein
- Length
- 2,363 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody C1; Spike protein S1; Omi-31 heavy chain; Omi-31 light chain; Omi-18 heavy…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 9 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Nanobody C1 | protein | 123 | 7% helix, 50% strand | — |
| N | Nanobody C1 | protein | 124 | 7% helix, 50% strand | — |
| E, F | Spike protein S1 | protein | 195 | 18% helix, 30% strand | P0DTC2 |
| A, C | Omi-31 heavy chain | protein | 228 | 7% helix, 57% strand | — |
| B | Omi-31 light chain | protein | 212 | 7% helix, 48% strand | — |
| H, J | Omi-18 heavy chain | protein | 215 | 6% helix, 53% strand | — |
| L | Omi-18 light chain | protein | 208 | 7% helix, 50% strand | — |
| D | Omi-31 light chain | protein | 213 | 7% helix, 49% strand | — |
| K | Omi-18 light chain | protein | 207 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.71 | 0.82 | 56 | empty |
| 2 | 407 | 0.68 | 0.81 | 47 | empty |
| 3 | 270 | 0.62 | 0.80 | 39 | empty |
| 4 | 549 | 0.62 | 0.75 | 71 | empty |
| 5 | 370 | 0.61 | 0.78 | 45 | empty |
Interfaces
21 interfaces between chains.
- C–D · 1888 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1869 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1740 Ų buried · 18 hydrogen bonds · protein-protein
- K–J · 1715 Ų buried · 14 hydrogen bonds · protein-protein
- E–A · 898 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZFB · SARS-CoV-2 Omicron RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs · the same entry in another collection · chain M against M, 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 7ZFB · PDBe 7ZFB · UniProt P0DTC2
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