MolNFT v1 · #19104 · protein
S45-18 Fab unliganded
1Q9O · S45-2 Fab (IGG1K) heavy chain: “S45-18 Fab unliganded”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.62). MolNFT v1 #19104 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1Q9O
- Type
- protein
- Length
- 890 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S45-2 Fab (IGG1K) heavy chain; S45-2 Fab (IGG1K) light chain
- Ligands
- MG
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | S45-2 Fab (IGG1K) heavy chain | protein | 226 | 7% helix, 48% strand | — |
| A, C | S45-2 Fab (IGG1K) light chain | protein | 219 | 7% helix, 53% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.62 | 0.74 | 65 | empty |
| 2 | 557 | 0.62 | 0.75 | 56 | empty |
| 3 | 55 | 0.54 | 0.89 | 18 | empty |
| 4 | 87 | 0.52 | 0.84 | 24 | empty |
| 5 | 177 | 0.50 | 0.78 | 29 | empty |
Interfaces
3 interfaces between chains.
- D–C · 2014 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 1940 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1Q9O · S45-18 Fab Unliganded · the same entry in another collection · chain B against B, 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 1Q9O · PDBe 1Q9O
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