MolNFT v1 · #128040 · protein
Localised reconstruction of alpha V beta 6 bound to foot and mouth disease virus O panasia - pose a prime.
5NER · O panasia VP1: “Localised reconstruction of alpha V beta 6 bound to foot and mouth disease virus O panasia - pose a prime.”. Electron microscopy, 3 ligands (MAN, NAG, CA), 16 pockets (best druggability 0.81). MolNFT v1 #128040 on…
- PDB
- 5NER
- Type
- protein
- Length
- 1,727 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O panasia VP1; O panasia VP2; O panasia VP3; O panasia VP4; Integrin alpha-V; Integrin…
- UniProt
- A0A1P8NWT0, A0A1B0SZV3, J3T9N5, A6Y878, P06756, P18564
- Ligands
- MAN, NAG, CA
- Pockets
- 16 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | O panasia VP1 | protein | 210 | 14% helix, 30% strand | A0A1P8NWT0 |
| 2 | O panasia VP2 | protein | 214 | 6% helix, 45% strand | A0A1B0SZV3 |
| 3 | O panasia VP3 | protein | 220 | 10% helix, 33% strand | J3T9N5 |
| 4 | O panasia VP4 | protein | 46 | 24% helix, 4% strand | A6Y878 |
| 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
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains 2, 3, A, 1
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.81 | 0.85 | 64 | empty |
| 2 | 142 | 0.60 | 0.84 | 27 | empty |
| 3 | 332 | 0.58 | 0.77 | 48 | empty |
| 4 | 92 | 0.53 | 0.84 | 22 | empty |
| 5 | 215 | 0.50 | 0.76 | 43 | empty |
Interfaces
9 interfaces between chains.
- 1–3 · 3633 Ų buried · 48 hydrogen bonds · protein-protein
- 1–2 · 1684 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1679 Ų buried · 13 hydrogen bonds · protein-protein
- 2–3 · 1460 Ų buried · 18 hydrogen bonds · protein-protein
- 3–4 · 1245 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 4 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5NER · Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O… · 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 A0A1P8NWT0
- Every structure of UniProt A0A1B0SZV3
- Every structure of UniProt J3T9N5
- Every structure of UniProt A6Y878
- Every structure of UniProt P06756
- Every structure of UniProt P18564
- Elsewhere: RCSB PDB 5NER · PDBe 5NER · UniProt A0A1P8NWT0 · UniProt A0A1B0SZV3 · UniProt J3T9N5 · UniProt A6Y878 · UniProt P06756 · UniProt P18564
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