MolNFT v1 · #62722 · protein
Structure of the Fab fragment of gc-1008 in complex with transforming growth factor-beta 3
3EO1 · Gc-1008 Fab light chain: “Structure of the Fab fragment of gc-1008 in complex with transforming growth factor-beta 3”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #62722 on GenesisL1: 3D structure, binding…
- PDB
- 3EO1
- Type
- protein
- Length
- 2,172 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gc-1008 Fab light chain; Gc-1008 Fab heavy chain; Transforming growth factor beta-3
- UniProt
- P10600
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Gc-1008 Fab light chain | protein | 215 | 5% helix, 47% strand | — |
| B, E, H, K | Gc-1008 Fab heavy chain | protein | 216 | 1% helix, 45% strand | — |
| C, F, I, L | Transforming growth factor beta-3 | protein | 112 | 21% helix, 42% strand | P10600 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.79 | 0.88 | 34 | empty |
| 2 | 265 | 0.67 | 0.83 | 47 | empty |
| 3 | 454 | 0.60 | 0.75 | 53 | empty |
| 4 | 342 | 0.56 | 0.75 | 52 | empty |
| 5 | 370 | 0.56 | 0.74 | 43 | empty |
Interfaces
21 interfaces between chains.
- G–H · 1814 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1813 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1744 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 1736 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1248 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide (disulfide).
Compared structures
- 3EO1 · Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3 · the same entry in another collection · chain L against L, 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 P10600
- Elsewhere: RCSB PDB 3EO1 · PDBe 3EO1 · UniProt P10600
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