MolNFT v1 · #121647 · protein
Crystal structure of human germline antibody IGHV5-51/IGKV4-1
5I1L · Fab light chain: “Crystal structure of human germline antibody IGHV5-51/IGKV4-1”. X-ray diffraction, 9 pockets (best druggability 0.74). MolNFT v1 #121647 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I1L
- Type
- protein
- Length
- 877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab light chain | protein | 220 | 6% helix, 52% strand | — |
| H | Fab heavy chain | protein | 225 | 8% helix, 49% strand | — |
| A | Fab light chain | protein | 219 | 6% helix, 53% strand | — |
| B | Fab heavy chain | protein | 213 | 9% helix, 54% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains L, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.74 | 0.81 | 74 | empty |
| 2 | 375 | 0.56 | 0.74 | 50 | empty |
| 3 | 307 | 0.54 | 0.75 | 41 | empty |
| 4 | 59 | 0.51 | 0.87 | 22 | empty |
| 5 | 165 | 0.49 | 0.77 | 30 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1876 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1721 Ų buried · 11 hydrogen bonds · protein-protein
- L–B · 367 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 164 Ų buried · 1 hydrogen bond · protein-protein
- H–B · 163 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5I1L · Crystal structure of human germline antibody IGHV5-51/IGKV4-1 · 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 5I1L · PDBe 5I1L
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