Research workbench
Localised reconstruction of integrin alpha V beta 6 bound to foot and mouth disease virus O1 manisa - pose a.
Analyse Localised reconstruction of integrin alpha V beta 6 bound to foot and mouth… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NET
- Type
- protein
- Length
- 1,717 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O1 manisa VP1; O1 manisa VP2; O1 manisa VP3; O1 manisa VP4; Integrin alpha-V; Integrin…
- UniProt
- Q6PMW3, Q80B23, E1ACS1, P06756, P18564
- Ligands
- NAG, MAN, CA
- Pockets
- 18 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | O1 manisa VP1 | protein | 208 | 11% helix, 28% strand | Q6PMW3 |
| 2 | O1 manisa VP2 | protein | 207 | 8% helix, 41% strand | Q6PMW3 |
| 3 | O1 manisa VP3 | protein | 220 | 7% helix, 35% strand | Q80B23 |
| 4 | O1 manisa VP4 | protein | 45 | 16% helix, 4% strand | E1ACS1 |
| A | Integrin alpha-V | protein | 589 | 5% helix, 42% strand | P06756 |
| B | Integrin beta-6 | protein | 448 | 21% helix, 29% strand | P18564 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A, 2, 3
- CA · Calcium ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.80 | 0.85 | 63 | empty |
| 2 | 444 | 0.61 | 0.76 | 43 | empty |
| 3 | 130 | 0.57 | 0.83 | 23 | empty |
| 4 | 126 | 0.57 | 0.84 | 27 | empty |
| 5 | 292 | 0.55 | 0.76 | 38 | empty |
Interfaces
9 interfaces between chains.
- 1–3 · 3648 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 1675 Ų buried · 13 hydrogen bonds · protein-protein
- 1–2 · 1492 Ų buried · 25 hydrogen bonds · protein-protein
- 2–3 · 1486 Ų buried · 16 hydrogen bonds · protein-protein
- 3–4 · 1148 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 4 glycan, 2 isopeptide (disulfide, N-glycosylation, glycosylation, isopeptide).
Compared structures
- 5NET · Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus… · the same entry in another collection · chain B against B, 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 0.99
- P18564 · AlphaFold monomer V2.0 prediction for integrin beta-6 (P18564) · a predicted model of the same protein · chain B against A, TM-score 0.55
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 Q6PMW3
- Every structure of UniProt Q80B23
- Every structure of UniProt E1ACS1
- Every structure of UniProt P06756
- Every structure of UniProt P18564
- Elsewhere: RCSB PDB 5NET · PDBe 5NET · UniProt Q6PMW3 · UniProt Q80B23 · UniProt E1ACS1 · UniProt P06756 · UniProt P18564
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