Research workbench
Crystal structure of homo-specific diabody
Analyse Crystal structure of homo-specific diabody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GS1
- Type
- protein
- Length
- 3,175 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain; Diabody
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M, O, Q | Light chain | protein | 106 | 6% helix, 46% strand | — |
| B, N, P, R | Heavy chain | protein | 118 | 10% helix, 53% strand | — |
| C, D, E, F, I, J, K, L | Diabody | protein | 229 | 9% helix, 48% strand | — |
| G | Diabody | protein | 223 | 5% helix, 49% strand | — |
| H | Diabody | protein | 224 | 5% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.73 | 0.80 | 63 | empty |
| 2 | 611 | 0.72 | 0.79 | 64 | empty |
| 3 | 789 | 0.72 | 0.77 | 99 | empty |
| 4 | 991 | 0.70 | 0.75 | 89 | empty |
| 5 | 887 | 0.67 | 0.74 | 77 | empty |
Interfaces
37 interfaces between chains.
- I–J · 2099 Ų buried · 31 hydrogen bonds · protein-protein
- K–L · 2093 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2084 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2053 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2026 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 5GS1 · Crystal structure of homo-specific diabody · 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 5GS1 · PDBe 5GS1
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