MolNFT v1 · #116506 · protein
Structure of the eleventh type III domain from human fibronectin
5DFT: “Structure of the eleventh type III domain from human fibronectin”. X-ray diffraction, 9 pockets (best druggability 0.74). MolNFT v1 #116506 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DFT
- Type
- protein
- Length
- 885 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibronectin
- UniProt
- P02751
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, J | Fibronectin | protein | 89 | 0% helix, 53% strand | P02751 |
| B, F, G, H, I | Fibronectin | protein | 88 | 0% helix, 53% strand | P02751 |
Ligands and binding sites
- CIT · Citric acid · additive · chains D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.74 | 0.80 | 80 | empty |
| 2 | 617 | 0.74 | 0.81 | 75 | CIT |
| 3 | 545 | 0.72 | 0.80 | 57 | empty |
| 4 | 540 | 0.72 | 0.80 | 67 | empty |
| 5 | 544 | 0.70 | 0.79 | 62 | empty |
Interfaces
19 interfaces between chains.
- A–E · 428 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 416 Ų buried · 4 hydrogen bonds · protein-protein
- F–J · 414 Ų buried · 5 hydrogen bonds · protein-protein
- G–I · 410 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 405 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 P02751
- Elsewhere: RCSB PDB 5DFT · PDBe 5DFT · UniProt P02751
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