Research workbench
Integrin ALPHAVBETA3 ectodomain bound to HR10 variant of the 10TH domain of fibronectin.
Analyse Integrin ALPHAVBETA3 ectodomain bound to HR10 variant of the 10TH domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NAJ
- Type
- protein
- Length
- 1,700 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-3; Fibronectin, HR10 variant
- UniProt
- P06756, P05106, P02751
- Ligands
- NAG, BMA, MAN, MN
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 920 | 2% helix, 43% strand | P06756 |
| B | Integrin beta-3 | protein | 690 | 17% helix, 25% strand | P05106 |
| C | Fibronectin, HR10 variant | protein | 90 | 0% helix, 44% strand | P02751 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.81 | 0.83 | 97 | empty |
| 2 | 885 | 0.79 | 0.82 | 98 | empty |
| 3 | 608 | 0.77 | 0.83 | 57 | empty |
| 4 | 365 | 0.70 | 0.82 | 44 | empty |
| 5 | 464 | 0.63 | 0.76 | 45 | NAG |
Interfaces
3 interfaces between chains.
- A–B · 3556 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 676 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 218 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 14 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 6NAJ · Integrin AlphaVBeta3 ectodomain bound to Hr10 variant of the 10th domain of Fibronectin. · the same entry in another collection · chain A against A, TM-score 1.00
- P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P02751 · AlphaFold monomer V2.0 prediction for fibronectin (P02751) · a predicted model of the same protein · chain C against A, TM-score 0.82
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 P06756
- Every structure of UniProt P05106
- Every structure of UniProt P02751
- Elsewhere: RCSB PDB 6NAJ · PDBe 6NAJ · UniProt P06756 · UniProt P05106 · UniProt P02751
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