Research workbench
3H5 Fab bound to ediii of denv 2 xtal form 1
Analyse 3H5 Fab bound to ediii of denv 2 xtal form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FLA
- Type
- protein
- Length
- 1,058 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain; Light chain of 3H5; Domain III of dengue virus 2
- UniProt
- P14340, P29991
- Ligands
- CL
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain | protein | 212 | 8% helix, 53% strand | — |
| B, L | Light chain of 3H5 | protein | 216 | 6% helix, 54% strand | — |
| G | Domain III of dengue virus 2 | protein | 98 | 0% helix, 49% strand | P14340 |
| H | Heavy chain | protein | 217 | 7% helix, 52% strand | — |
| I | Domain III of dengue virus 2 | protein | 99 | 0% helix, 48% strand | P29991 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, H, L
- GOL · Glycerol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.65 | 0.75 | 64 | empty |
| 2 | 681 | 0.65 | 0.74 | 73 | GOL |
| 3 | 194 | 0.56 | 0.80 | 32 | empty |
| 4 | 138 | 0.49 | 0.79 | 24 | empty |
| 5 | 163 | 0.49 | 0.77 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1732 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1713 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 576 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 561 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 481 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6FLA · 3H5 Fab bound to EDIII of DenV 2 Xtal form 1 · 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
- Every structure of UniProt P14340
- Every structure of UniProt P29991
- Elsewhere: RCSB PDB 6FLA · PDBe 6FLA · UniProt P14340 · UniProt P29991
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