Research workbench
Structure of a fragment of human fibronectin containing the 10TH, 11TH and 12TH type III domains
Analyse Structure of a fragment of human fibronectin containing the 10TH, 11TH and 12TH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XAY
- Type
- protein
- Length
- 1,084 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibronectin
- UniProt
- P02751
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibronectin | protein | 272 | 0% helix, 52% strand | P02751 |
| B | Fibronectin | protein | 269 | 0% helix, 54% strand | P02751 |
| C | Fibronectin | protein | 271 | 0% helix, 48% strand | P02751 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.64 | 0.80 | 47 | empty |
| 2 | 471 | 0.63 | 0.77 | 41 | empty |
| 3 | 76 | 0.63 | 0.91 | 20 | empty |
| 4 | 336 | 0.63 | 0.79 | 46 | empty |
| 5 | 204 | 0.62 | 0.83 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1861 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1850 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 487 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 484 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XAY · Structure of a fragment of human fibronectin containing the 10th, 11th and 12th type III… · the same entry in another collection · chain D against D, TM-score 1.00
- P02751 · AlphaFold monomer V2.0 prediction for fibronectin (P02751) · a predicted model of the same protein · chain C against A, TM-score 0.66
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 6XAY · PDBe 6XAY · UniProt P02751
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