Research workbench
Structure of the transforming growth factor-beta neutralizing antibody gc-1008
Analyse Structure of the transforming growth factor-beta neutralizing antibody gc-1008 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EO0
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gc-1008 Fab light chain; Gc-1008 Fab heavy chain
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gc-1008 Fab light chain | protein | 215 | 7% helix, 50% strand | — |
| B, D | Gc-1008 Fab heavy chain | protein | 220 | 7% helix, 51% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.73 | 0.79 | 70 | empty |
| 2 | 473 | 0.62 | 0.76 | 58 | empty |
| 3 | 441 | 0.59 | 0.75 | 48 | empty |
| 4 | 59 | 0.48 | 0.85 | 18 | empty |
| 5 | 100 | 0.39 | 0.76 | 24 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1787 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1786 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 402 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3EO0 · Structure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008 · 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 3EO0 · PDBe 3EO0
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