MolNFT v1 · #181714 · protein
Structure of SARS-cov-2 spike protein receptor binding domain in complex with a neutralizing antibody, CV2-75 Fab
7M3I · CV2-75 Fab heavy chain: “Structure of SARS-cov-2 spike protein receptor binding domain in complex with a neutralizing antibody, CV2-75…”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.77). MolNFT v1 #181714 on…
- PDB
- 7M3I
- Type
- protein
- Length
- 1,282 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CV2-75 Fab heavy chain; CV2-75 Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CV2-75 Fab heavy chain | protein | 221 | 5% helix, 50% strand | — |
| B, L | CV2-75 Fab light chain | protein | 211 | 8% helix, 50% strand | — |
| C, R | Spike protein S1 | protein | 217 | 14% helix, 26% strand | P0DTC2 |
| H | CV2-75 Fab heavy chain | protein | 205 | 4% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.77 | 0.82 | 88 | empty |
| 2 | 723 | 0.72 | 0.78 | 51 | empty |
| 3 | 755 | 0.68 | 0.76 | 63 | empty |
| 4 | 398 | 0.63 | 0.77 | 49 | empty |
| 5 | 144 | 0.61 | 0.84 | 31 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1748 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1676 Ų buried · 18 hydrogen bonds · protein-protein
- C–R · 603 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 540 Ų buried · 9 hydrogen bonds · protein-protein
- H–R · 525 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 7M3I · Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a… · 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 7M3I · PDBe 7M3I · UniProt P0DTC2
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