Research workbench
Structure of legionella pneumophila degq (S190A variant)
Analyse Structure of legionella pneumophila degq (S190A variant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YNN
- Type
- protein
- Length
- 3,272 residues
- Chains
- 22
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease do; Octapeptide; Hexa-peptide; Hepta-peptide; Unk-unk-unk
- EC
- 3.4.21.-
- UniProt
- Q5ZVV9
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H | Protease do (EC 3.4.21.-) | protein | 400 | 19% helix, 41% strand | Q5ZVV9 |
| B | Protease do (EC 3.4.21.-) | protein | 399 | 19% helix, 42% strand | Q5ZVV9 |
| I | Octapeptide | protein | 8 | 0% helix, 50% strand | — |
| J, L | Hexa-peptide | protein | 6 | 0% helix, 33% strand | — |
| K, M, N, O, P | Hepta-peptide | protein | 7 | 0% helix, 43% strand | — |
| Q, R, S, T, U, V | Unk-unk-unk | protein | 3 | 0% helix, 33% strand | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.78 | 0.98 | 25 | empty |
| 2 | 99 | 0.76 | 0.97 | 24 | empty |
| 3 | 511 | 0.68 | 0.79 | 61 | empty |
| 4 | 51 | 0.68 | 0.97 | 21 | empty |
| 5 | 50 | 0.65 | 0.96 | 21 | empty |
Interfaces
25 interfaces between chains.
- A–D · 1339 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 1314 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 1299 Ų buried · 16 hydrogen bonds · protein-protein
- D–H · 1291 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 1270 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4YNN · Structure of Legionella pneumophila DegQ (S190A variant) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5ZVV9
- Elsewhere: RCSB PDB 4YNN · PDBe 4YNN · UniProt Q5ZVV9
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