Research workbench
Integrin ALPHAVBETA3 ectodomain bound to an antagonistic tenth domain of fibronectin
Analyse Integrin ALPHAVBETA3 ectodomain bound to an antagonistic tenth domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MMZ
- Type
- protein
- Length
- 1,701 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-3; Fibronectin
- UniProt
- P06756, P05106, P02751
- Ligands
- NAG, BMA, MAN, MN, NA, CL
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 920 | 2% helix, 45% strand | P06756 |
| B | Integrin beta-3 | protein | 690 | 17% helix, 25% strand | P05106 |
| C | Fibronectin | protein | 91 | 0% helix, 44% strand | P02751 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 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
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 840 | 0.81 | 0.83 | 94 | empty |
| 2 | 1164 | 0.77 | 0.79 | 103 | empty |
| 3 | 601 | 0.77 | 0.83 | 57 | empty |
| 4 | 664 | 0.70 | 0.78 | 60 | empty |
| 5 | 419 | 0.62 | 0.77 | 44 | NA, CL |
Interfaces
3 interfaces between chains.
- A–B · 3543 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 599 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 206 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 4MMZ · Integrin AlphaVBeta3 ectodomain bound to an antagonistic tenth 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 0.81
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 4MMZ · PDBe 4MMZ · UniProt P06756 · UniProt P05106 · UniProt P02751
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