Research workbench
Unliganded 2 crystal structure of S25-26 Fab
Analyse Unliganded 2 crystal structure of S25-26 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M93
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S25-26 Fab (IGG1K) light chain; S25-26 Fab (IGG1K) heavy chain
- Ligands
- NAG, CA
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, C | S25-26 Fab (IGG1K) light chain | protein | 218 | 6% helix, 54% strand | — |
| H, B | S25-26 Fab (IGG1K) heavy chain | protein | 218 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H, B
- CA · Calcium ion · metal · chains B
- ACT · Acetate ion · additive · 3 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.67 | 0.75 | 85 | empty |
| 2 | 285 | 0.59 | 0.78 | 48 | ACT |
| 3 | 232 | 0.55 | 0.78 | 35 | empty |
| 4 | 155 | 0.52 | 0.79 | 25 | empty |
| 5 | 304 | 0.51 | 0.73 | 37 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2046 Ų buried · 24 hydrogen bonds · protein-protein
- C–B · 2042 Ų buried · 20 hydrogen bonds · protein-protein
- H–C · 552 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4M93 · Unliganded 2 crystal structure of S25-26 Fab · 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 4M93 · PDBe 4M93
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