Research workbench
Crystal structure of fibroblast growth factor 19 in complex with Fab
Analyse Crystal structure of fibroblast growth factor 19 in complex with Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KTR
- Type
- protein
- Length
- 1,118 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G1A8-Fab-hc; G1A8-Fab-lc; Fibroblast growth factor 19
- UniProt
- O95750
- Ligands
- NA, SO4
- Pockets
- 12 · best druggability 0.51
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G1A8-Fab-hc | protein | 211 | 4% helix, 53% strand | — |
| B | G1A8-Fab-lc | protein | 213 | 6% helix, 50% strand | — |
| C, D | Fibroblast growth factor 19 | protein | 136 | 12% helix, 43% strand | O95750 |
| F | G1A8-Fab-hc | protein | 210 | 6% helix, 53% strand | — |
| G | G1A8-Fab-lc | protein | 212 | 6% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains F, G
- SO4 · Sulfate ion · ion · 10 copies · chains B, C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.51 | 0.81 | 18 | empty |
| 2 | 105 | 0.49 | 0.81 | 23 | empty |
| 3 | 183 | 0.48 | 0.76 | 35 | empty |
| 4 | 217 | 0.46 | 0.73 | 46 | empty |
| 5 | 193 | 0.44 | 0.73 | 36 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1601 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1594 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 638 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 620 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 610 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6KTR · Crystal structure of fibroblast growth factor 19 in complex with Fab · the same entry in another collection · chain G against G, TM-score 1.00
- O95750 · AlphaFold monomer V2.0 prediction for fibroblast growth factor 19 (O95750) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 O95750
- Elsewhere: RCSB PDB 6KTR · PDBe 6KTR · UniProt O95750
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