Research workbench
Crystal structure of 10E8 ghv-glv antigen-binding fragment.
Analyse Crystal structure of 10E8 ghv-glv antigen-binding fragment. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JO5
- Type
- protein
- Length
- 1,732 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10E8 ghv; 10E8 glv
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, C, E | 10E8 ghv | protein | 221 | 10% helix, 52% strand | — |
| L, B, D, F | 10E8 glv | protein | 212 | 8% helix, 50% strand | — |
| A | 10E8 ghv | protein | 221 | 10% helix, 52% strand | — |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.67 | 0.76 | 62 | empty |
| 2 | 701 | 0.66 | 0.75 | 65 | empty |
| 3 | 618 | 0.65 | 0.76 | 61 | empty |
| 4 | 596 | 0.65 | 0.76 | 55 | empty |
| 5 | 261 | 0.55 | 0.77 | 50 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2012 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1935 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1916 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1877 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 259 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5JO5 · Crystal structure of 10E8 gHV-gLV antigen-binding fragment. · the same entry in another collection · chain H against H, 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 5JO5 · PDBe 5JO5
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