MolNFT v1 · #188609 · protein
Local refinement of cryo-EM structure of the interface of the omicron rbd in complex with antibodies B-182.1 and A19-46.1
7U0D · Surface glycoprotein: “Local refinement of cryo-EM structure of the interface of the omicron rbd in complex with antibodies B-182.1…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.80). MolNFT v1 #188609 on…
- PDB
- 7U0D
- Type
- protein
- Length
- 1,071 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface glycoprotein; Heavy chain of SARS-cov-2 antibody A19-46.1; Light chain of…
- UniProt
- A0A7U3CI26
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 6% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Surface glycoprotein | protein | 196 | 12% helix, 18% strand | A0A7U3CI26 |
| M | Heavy chain of SARS-cov-2 antibody A19-46.1 | protein | 231 | 6% helix, 48% strand | — |
| N | Light chain of SARS-cov-2 antibody A19-46.1 | protein | 216 | 10% helix, 51% strand | — |
| O | Heavy chain of SARS-cov-2 antibody B1-182.1 | protein | 215 | 1% helix, 31% strand | — |
| P | Light chain of SARS-cov-2 antibody B1-182.1 | protein | 213 | 2% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.80 | 0.88 | 64 | empty |
| 2 | 818 | 0.79 | 0.82 | 112 | empty |
| 3 | 83 | 0.73 | 0.95 | 16 | empty |
| 4 | 312 | 0.67 | 0.82 | 47 | empty |
| 5 | 682 | 0.67 | 0.76 | 89 | empty |
Interfaces
8 interfaces between chains.
- M–N · 1785 Ų buried · 11 hydrogen bonds · protein-protein
- O–P · 1489 Ų buried · 6 hydrogen bonds · protein-protein
- B–N · 502 Ų buried · 6 hydrogen bonds · protein-protein
- B–O · 488 Ų buried · 6 hydrogen bonds · protein-protein
- B–M · 389 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7U0D · Local refinement of cryo-EM structure of the interface of the Omicron RBD in complex with… · the same entry in another collection · chain B against B, 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 A0A7U3CI26
- Elsewhere: RCSB PDB 7U0D · PDBe 7U0D · UniProt A0A7U3CI26
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