MolNFT v2 · #218120 · protein
CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus
8QQJ · Type IV narrow pilus major component PilA5: “CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus”. Electron microscopy at 2.63, 4 ligands (A2G, MAN, WT8), 20 pockets (best druggability 0.73). MolNFT v2 #218120 on…
- PDB
- 8QQJ
- Type
- protein
- Length
- 3,441 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.63
- Source
- Thermus thermophilus HB27
- Molecule
- Type IV narrow pilus major component PilA5
- UniProt
- Q72GL2
- Ligands
- A2G, MAN, WT8, MG
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · resolution 2.63 · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, A, B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e | Type IV narrow pilus major component PilA5 | protein | 111 | 41% helix, 23% strand | Q72GL2 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 62 copies · chains J, A, B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e
- MAN · alpha-D-mannopyranose · sugar · 31 copies
- WT8 · 7-Acetamido-5-acetimidoyl-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic aci · sugar · 31 copies
- MG · Magnesium ion · metal · 31 copies · chains J, A, B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.73 | 0.77 | 56 | empty |
| 2 | 54 | 0.72 | 0.98 | 17 | empty |
| 3 | 53 | 0.72 | 0.98 | 23 | empty |
| 4 | 52 | 0.71 | 0.98 | 19 | empty |
| 5 | 54 | 0.70 | 0.97 | 23 | empty |
Interfaces
189 interfaces between chains.
- O–R · 1052 Ų buried · 8 hydrogen bonds · protein-protein
- P–S · 1052 Ų buried · 7 hydrogen bonds · protein-protein
- Z–c · 1051 Ų buried · 8 hydrogen bonds · protein-protein
- a–d · 1051 Ų buried · 8 hydrogen bonds · protein-protein
- Q–T · 1050 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 31 glycan (disulfide, O-glycosylation).
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 Q72GL2
- Elsewhere: RCSB PDB 8QQJ · PDBe 8QQJ · UniProt Q72GL2
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