Research workbench
Crystal structure of quinine-dependent Fab 314.3
Analyse Crystal structure of quinine-dependent Fab 314.3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UIM
- Type
- protein
- Length
- 1,747 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 314.3
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Fab 314.3 | protein | 224 | 4% helix, 49% strand | — |
| B, D, F, L | Fab 314.3 | protein | 214 | 6% helix, 52% strand | — |
| C | Fab 314.3 | protein | 221 | 4% helix, 52% strand | — |
| H | Fab 314.3 | protein | 222 | 4% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 778 | 0.72 | 0.78 | 77 | empty |
| 2 | 609 | 0.72 | 0.80 | 58 | empty |
| 3 | 340 | 0.63 | 0.79 | 51 | SO4 |
| 4 | 358 | 0.60 | 0.77 | 50 | empty |
| 5 | 344 | 0.54 | 0.74 | 43 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2051 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2039 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 2000 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1972 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 413 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 4UIM · crystal structure of quinine-dependent Fab 314.3 · the same entry in another collection · chain A against A, 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 4UIM · PDBe 4UIM
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