MolNFT v1 · #144817 · protein
Unliganded S25-5 Fab
6C5I · Fab IGG1 heavy chain: “Unliganded S25-5 Fab”. X-ray diffraction, 3 ligands (NAG, NI, CL), 3 pockets (best druggability 0.54). MolNFT v1 #144817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6C5I
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab IGG1 heavy chain; Fab IGG1 (kappa) light chain
- UniProt
- Q99LC4, A0A0F7R5U8
- Ligands
- NAG, NI, CL
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab IGG1 heavy chain | protein | 216 | 4% helix, 50% strand | Q99LC4 |
| L | Fab IGG1 (kappa) light chain | protein | 219 | 7% helix, 52% strand | A0A0F7R5U8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NI · Nickel (II) ion · metal · 2 copies · chains L, H
- CL · Chloride ion · ion · chains H
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.54 | 0.73 | 48 | PG0 |
| 2 | 141 | 0.44 | 0.76 | 23 | NI |
| 3 | 138 | 0.43 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- H–L · 1975 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6C5I · Unliganded S25-5 Fab · 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
- Every structure of UniProt Q99LC4
- Every structure of UniProt A0A0F7R5U8
- Elsewhere: RCSB PDB 6C5I · PDBe 6C5I · UniProt Q99LC4 · UniProt A0A0F7R5U8
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