MolNFT v1 · #187886 · protein
Crystal structure of S25-2 Fab unliganded 4
7T0K · S25-2 Fab light chain: “Crystal structure of S25-2 Fab unliganded 4”. X-ray diffraction, 1 ligand (IOD), 20 pockets (best druggability 0.69). MolNFT v1 #187886 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7T0K
- Type
- protein
- Length
- 1,752 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S25-2 Fab light chain; S25-2 Fab heavy chain
- Ligands
- IOD
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, C | S25-2 Fab light chain | protein | 218 | 6% helix, 52% strand | — |
| H | S25-2 Fab heavy chain | protein | 218 | 10% helix, 49% strand | — |
| A, E | S25-2 Fab light chain | protein | 219 | 6% helix, 54% strand | — |
| B | S25-2 Fab heavy chain | protein | 223 | 7% helix, 49% strand | — |
| D | S25-2 Fab heavy chain | protein | 222 | 7% helix, 49% strand | — |
| F | S25-2 Fab heavy chain | protein | 215 | 7% helix, 51% strand | — |
Ligands and binding sites
- IOD · Iodide ion · ion · 34 copies · chains L, H, B, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.69 | 0.80 | 62 | empty |
| 2 | 192 | 0.67 | 0.86 | 24 | IOD |
| 3 | 155 | 0.63 | 0.85 | 25 | IOD |
| 4 | 482 | 0.63 | 0.76 | 49 | IOD |
| 5 | 552 | 0.61 | 0.74 | 67 | IOD |
Interfaces
13 interfaces between chains.
- A–B · 2001 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1961 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1843 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1767 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 416 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7T0K · Crystal structure of S25-2 Fab Unliganded 4 · 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 7T0K · PDBe 7T0K
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