Research workbench
Crystal structure of the 2F5 Fab'-3H6 Fab complex
Analyse Crystal structure of the 2F5 Fab'-3H6 Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BQU
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2F5 Fab' light chain; 2F5 Fab' heavy chain; 3H6 Fab light chain; 3H6 Fab heavy chain
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2F5 Fab' light chain | protein | 211 | 4% helix, 48% strand | — |
| B | 2F5 Fab' heavy chain | protein | 214 | 4% helix, 50% strand | — |
| C | 3H6 Fab light chain | protein | 186 | 5% helix, 48% strand | — |
| D | 3H6 Fab heavy chain | protein | 217 | 7% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.62 | 0.75 | 61 | SO4 |
| 2 | 532 | 0.60 | 0.74 | 58 | empty |
| 3 | 174 | 0.57 | 0.81 | 32 | empty |
| 4 | 389 | 0.56 | 0.74 | 58 | empty |
| 5 | 65 | 0.31 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1802 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1768 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 478 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 214 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3BQU · Crystal Structure of the 2F5 Fab'-3H6 Fab Complex · 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 3BQU · PDBe 3BQU
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