MolNFT v1 · #175943 · protein
A neutralizing mab targeting receptor-binding-domain of SARS-cov-2
7D6I · Spike protein S1: “A neutralizing mab targeting receptor-binding-domain of SARS-cov-2”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.62). MolNFT v1 #175943 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7D6I
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Heavy chain of GH12-Fab; Light chain of GH12-Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 200 | 16% helix, 27% strand | P0DTC2 |
| B | Heavy chain of GH12-Fab | protein | 212 | 4% helix, 48% strand | — |
| C | Light chain of GH12-Fab | protein | 215 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.62 | 0.74 | 57 | empty |
| 2 | 131 | 0.47 | 0.79 | 20 | empty |
| 3 | 153 | 0.44 | 0.75 | 27 | empty |
| 4 | 117 | 0.42 | 0.76 | 22 | empty |
| 5 | 105 | 0.36 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1689 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 449 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 364 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7D6I · A neutralizing MAb targeting receptor-binding-domain of SARS-CoV-2 · 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 7D6I · PDBe 7D6I · UniProt P0DTC2
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