Research workbench
PB3 domain of human PLK4 (apo)
Analyse PB3 domain of human PLK4 (apo) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LHY
- Type
- protein
- Length
- 4,620 residues
- Chains
- 60
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK4
- EC
- 2.7.11.21
- UniProt
- O00444
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y | SERINE/THREONINE-protein kinase PLK4 (EC 2.7.11.21) | protein | 77 | 9% helix, 53% strand | O00444 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.90 | 0.93 | 103 | empty |
| 2 | 859 | 0.90 | 0.92 | 111 | empty |
| 3 | 1140 | 0.89 | 0.90 | 125 | empty |
| 4 | 1176 | 0.89 | 0.90 | 127 | empty |
| 5 | 1169 | 0.89 | 0.90 | 121 | empty |
Interfaces
226 interfaces between chains.
- h–i · 1329 Ų buried · 24 hydrogen bonds · protein-protein
- Y–Z · 1311 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1309 Ų buried · 22 hydrogen bonds · protein-protein
- O–P · 1308 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1303 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5LHY · PB3 Domain of Human PLK4 (apo) · 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 O00444
- Elsewhere: RCSB PDB 5LHY · PDBe 5LHY · UniProt O00444
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