MolNFT v1 · #157788 · protein
Integrin ALPHAVBETA3 ectodomain bound to HR10 variant of the 10TH domain of fibronectin.
6NAJ · Integrin alpha-V: “Integrin ALPHAVBETA3 ectodomain bound to HR10 variant of the 10TH domain of fibronectin.”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 18 pockets (best druggability 0.81). MolNFT v1 #157788 on GenesisL1: 3D…
- 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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