MolNFT v1 · #169239 · protein
Crystal structure of a lewis-binding Fab (CH88.2)
6X5E · CH88.2 Fab light chain: “Crystal structure of a lewis-binding Fab (CH88.2)”. X-ray diffraction, 1 ligand (NI), 8 pockets (best druggability 0.58). MolNFT v1 #169239 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6X5E
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH88.2 Fab light chain; CH88.2 Fab heavy chain
- Ligands
- NI
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | CH88.2 Fab light chain | protein | 213 | 4% helix, 49% strand | — |
| H | CH88.2 Fab heavy chain | protein | 219 | 3% helix, 53% strand | — |
| A | CH88.2 Fab light chain | protein | 214 | 5% helix, 50% strand | — |
| B | CH88.2 Fab heavy chain | protein | 221 | 5% helix, 51% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.58 | 0.75 | 49 | empty |
| 2 | 451 | 0.58 | 0.74 | 61 | empty |
| 3 | 295 | 0.57 | 0.77 | 40 | empty |
| 4 | 71 | 0.48 | 0.84 | 26 | empty |
| 5 | 145 | 0.46 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1792 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1712 Ų buried · 12 hydrogen bonds · protein-protein
- L–A · 223 Ų buried · 3 hydrogen bonds · protein-protein
- H–A · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6X5E · Crystal structure of a Lewis-binding Fab (ch88.2) · 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 6X5E · PDBe 6X5E
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