MolNFT v1 · #179539 · protein
Crystal structure of an anti-SARS-cov-2 human neutralizing antibody Fab fragment, C002
7K8O · C002 Fab heavy chain: “Crystal structure of an anti-SARS-cov-2 human neutralizing antibody Fab fragment, C002”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.57). MolNFT v1 #179539 on GenesisL1: 3D structure…
- PDB
- 7K8O
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C002 Fab heavy chain; C002 Fab light chain
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | C002 Fab heavy chain | protein | 226 | 7% helix, 50% strand | — |
| L | C002 Fab light chain | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.57 | 0.79 | 32 | empty |
| 2 | 295 | 0.53 | 0.75 | 45 | empty |
| 3 | 137 | 0.44 | 0.76 | 29 | GOL |
| 4 | 84 | 0.33 | 0.74 | 25 | GOL |
| 5 | 53 | 0.29 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- H–L · 1969 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7K8O · Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C002 · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 7K8O · PDBe 7K8O
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