MolNFT v1 · #109361 · protein
Engineered Fab fragment specific for eympme (ee) peptide
4X0K · Fab fragment heavy chain: “Engineered Fab fragment specific for eympme (ee) peptide”. X-ray diffraction, 12 pockets (best druggability 0.57). MolNFT v1 #109361 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4X0K
- Type
- protein
- Length
- 916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment heavy chain; Fab fragment light chain
- Pockets
- 12 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab fragment heavy chain | protein | 229 | 8% helix, 52% strand | — |
| L | Fab fragment light chain | protein | 226 | 5% helix, 49% strand | — |
| A | Fab fragment heavy chain | protein | 235 | 9% helix, 51% strand | — |
| B | Fab fragment light chain | protein | 226 | 6% helix, 49% strand | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.57 | 0.78 | 32 | empty |
| 2 | 190 | 0.56 | 0.79 | 29 | empty |
| 3 | 59 | 0.55 | 0.89 | 17 | empty |
| 4 | 60 | 0.53 | 0.88 | 21 | empty |
| 5 | 315 | 0.53 | 0.74 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2444 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 2305 Ų buried · 27 hydrogen bonds · protein-protein
- L–B · 237 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4X0K · Engineered Fab fragment specific for EYMPME (EE) 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
- Elsewhere: RCSB PDB 4X0K · PDBe 4X0K
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