Research workbench
Crystal structure of S25-2 Fab unliganded 3
Analyse Crystal structure of S25-2 Fab unliganded 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T0J
- Type
- protein
- Length
- 1,743 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
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A, E | S25-2 Fab light chain | protein | 218 | 6% helix, 53% strand | — |
| H | S25-2 Fab heavy chain | protein | 223 | 8% helix, 49% strand | — |
| B | S25-2 Fab heavy chain | protein | 214 | 7% helix, 50% strand | — |
| C | S25-2 Fab light chain | protein | 219 | 6% helix, 54% strand | — |
| D | S25-2 Fab heavy chain | protein | 214 | 7% helix, 51% strand | — |
| F | S25-2 Fab heavy chain | protein | 219 | 7% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.77 | 0.96 | 31 | empty |
| 2 | 967 | 0.75 | 0.78 | 99 | empty |
| 3 | 84 | 0.75 | 0.97 | 28 | empty |
| 4 | 113 | 0.68 | 0.91 | 26 | empty |
| 5 | 496 | 0.60 | 0.75 | 50 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1953 Ų buried · 23 hydrogen bonds · protein-protein
- L–H · 1942 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1807 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1806 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 239 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7T0J · Crystal structure of S25-2 Fab Unliganded 3 · 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 7T0J · PDBe 7T0J
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