Research workbench
Crystal structure of the fourth and fifth fibronectin F1 modules in complex with a fragment of staphylococcus aureus fnbpa-1
Analyse Crystal structure of the fourth and fifth fibronectin F1 modules in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RKY
- Type
- protein
- Length
- 222 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibronectin; Fibronectin-binding protein
- UniProt
- P02751, P14738
- Ligands
- K, SCN
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibronectin | protein | 90 | 0% helix, 60% strand | P02751 |
| C | Fibronectin | protein | 92 | 0% helix, 61% strand | P02751 |
| B | Fibronectin-binding protein | protein | 21 | 0% helix, 57% strand | P14738 |
| D | Fibronectin-binding protein | protein | 19 | 0% helix, 58% strand | P14738 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.70 | 0.94 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–B · 1212 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1204 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 603 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 131 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2RKY · Crystal structure of the fourth and fifth fibronectin F1 modules in complex with a… · 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 0.81
- P14738 · AlphaFold monomer V2.0 prediction for fibronectin-binding protein a (P14738) · a predicted model of the same protein · chain D against A, TM-score 0.25
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
- Every structure of UniProt P14738
- Elsewhere: RCSB PDB 2RKY · PDBe 2RKY · UniProt P02751 · UniProt P14738
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