Research workbench
Crystal structure of antibody against schizophyllan in complex with laminarihexaose
Analyse Crystal structure of antibody against schizophyllan in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EV2
- Type
- protein
- Length
- 1,731 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain; Light chain
- Ligands
- BGC
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain | protein | 220 | 8% helix, 50% strand | — |
| B, D | Light chain | protein | 217 | 6% helix, 52% strand | — |
| C | Heavy chain | protein | 222 | 8% helix, 51% strand | — |
| E | Heavy chain | protein | 214 | 7% helix, 51% strand | — |
| F, H | Light chain | protein | 213 | 6% helix, 53% strand | — |
| G | Heavy chain | protein | 215 | 7% helix, 51% strand | — |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.62 | 0.76 | 57 | empty |
| 2 | 411 | 0.61 | 0.76 | 56 | empty |
| 3 | 87 | 0.55 | 0.86 | 20 | empty |
| 4 | 64 | 0.53 | 0.88 | 17 | empty |
| 5 | 57 | 0.53 | 0.89 | 22 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2083 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2003 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1839 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1800 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 448 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6EV2 · Crystal structure of antibody against schizophyllan in complex with laminarihexaose · the same entry in another collection · chain C against C, 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 6EV2 · PDBe 6EV2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.