MolNFT v1 · #182966 · protein
Crystal structure of human neutralizing mab CV3-25 binding to SARS- cov-2 S mper peptide 1140-1165
7NAB · CV3-25 Fab heavy chain: “Crystal structure of human neutralizing mab CV3-25 binding to SARS- cov-2 S mper peptide 1140-1165”. X-ray diffraction, 2 ligands (NA, NH2), 8 pockets (best druggability 0.67). MolNFT v1 #182966 on…
- PDB
- 7NAB
- Type
- protein
- Length
- 918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CV3-25 Fab heavy chain; CV3-25 Fab light chain; Spike protein S2
- UniProt
- P0DTC2
- Ligands
- NA, NH2
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | CV3-25 Fab heavy chain | protein | 226 | 8% helix, 54% strand | — |
| L, B | CV3-25 Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| D, C | Spike protein S2 | protein | 20 | 50% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- NA · Sodium ion · metal · 16 copies · chains H, L, A, B
- NH2 · Amino group · ion · 2 copies · chains D, C
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.67 | 0.77 | 79 | NA |
| 2 | 354 | 0.55 | 0.75 | 49 | empty |
| 3 | 354 | 0.55 | 0.74 | 43 | empty |
| 4 | 189 | 0.53 | 0.78 | 32 | NA |
| 5 | 106 | 0.35 | 0.73 | 30 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1911 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1860 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 671 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 655 Ų buried · 21 hydrogen bonds · protein-protein
- H–B · 359 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7NAB · Crystal structure of human neutralizing mAb CV3-25 binding to SARS-CoV-2 S MPER peptide… · 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 7NAB · PDBe 7NAB · UniProt P0DTC2
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