MolNFT v1 · #19102 · protein
S25-2 Fab unliganded 2
1Q9L · S25-2 Fab (IGG1K) heavy chain: “S25-2 Fab unliganded 2”. X-ray diffraction, 2 ligands (MG, ZN), 11 pockets (best druggability 0.79). MolNFT v1 #19102 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1Q9L
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S25-2 Fab (IGG1K) heavy chain; S25-2 Fab (IGG1K) light chain
- Ligands
- MG, ZN
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | S25-2 Fab (IGG1K) heavy chain | protein | 222 | 7% helix, 49% strand | — |
| A, C | S25-2 Fab (IGG1K) light chain | protein | 219 | 6% helix, 52% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains B, A, D, C
- ZN · Zinc ion · metal · 3 copies · chains A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.79 | 0.95 | 30 | MG |
| 2 | 220 | 0.77 | 0.91 | 37 | empty |
| 3 | 891 | 0.70 | 0.75 | 84 | empty |
| 4 | 651 | 0.64 | 0.74 | 74 | empty |
| 5 | 333 | 0.56 | 0.76 | 49 | empty |
Interfaces
4 interfaces between chains.
- D–C · 2006 Ų buried · 22 hydrogen bonds · protein-protein
- B–A · 1969 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 316 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1Q9L · S25-2 Fab Unliganded 2 · 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 1Q9L · PDBe 1Q9L
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