MolNFT v1 · #118364 · protein
Crystal structure of Fab of parasite invasion inhibitory antibody C1 - monoclinic form
5EZL · Fab C12: “Crystal structure of Fab of parasite invasion inhibitory antibody C1 - monoclinic form”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.73). MolNFT v1 #118364 on GenesisL1: 3D structure, binding sites…
- PDB
- 5EZL
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab C12
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Fab C12 | protein | 222 | 8% helix, 50% strand | — |
| B, L | Fab C12 | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.73 | 0.78 | 88 | empty |
| 2 | 64 | 0.53 | 0.87 | 21 | empty |
| 3 | 254 | 0.53 | 0.76 | 34 | empty |
| 4 | 164 | 0.51 | 0.78 | 24 | empty |
| 5 | 78 | 0.47 | 0.82 | 26 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1865 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1847 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 273 Ų buried · 3 hydrogen bonds · protein-protein
- B–L · 95 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5EZL · Crystal Structure of Fab of parasite invasion inhibitory antibody c1 - monoclinic form · 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
- Elsewhere: RCSB PDB 5EZL · PDBe 5EZL
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