MolNFT v1 · #141206 · protein
Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, thermomonospora curvata pkwa
5YZV · Probable SERINE/THREONINE-protein kinase pkwa: “Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein…”. X-ray diffraction, 5 pockets (best druggability 0.88). MolNFT v1 #141206 on…
- PDB
- 5YZV
- Type
- protein
- Length
- 1,436 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable SERINE/THREONINE-protein kinase pkwa
- EC
- 2.7.11.1
- UniProt
- P49695
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable SERINE/THREONINE-protein kinase pkwa (EC 2.7.11.1) | protein | 286 | 0% helix, 52% strand | P49695 |
| B, E | Probable SERINE/THREONINE-protein kinase pkwa (EC 2.7.11.1) | protein | 288 | 0% helix, 57% strand | P49695 |
| C | Probable SERINE/THREONINE-protein kinase pkwa (EC 2.7.11.1) | protein | 290 | 0% helix, 53% strand | P49695 |
| D | Probable SERINE/THREONINE-protein kinase pkwa (EC 2.7.11.1) | protein | 284 | 0% helix, 55% strand | P49695 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.88 | 0.89 | 103 | empty |
| 2 | 1156 | 0.88 | 0.89 | 103 | empty |
| 3 | 839 | 0.81 | 0.83 | 53 | empty |
| 4 | 332 | 0.58 | 0.76 | 34 | empty |
| 5 | 124 | 0.44 | 0.77 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 514 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 511 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 468 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 440 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YZV · Biophysical and structural characterization of the thermostable WD40 domain of a… · the same entry in another collection · chain E against E, TM-score 1.00
- P49695 · AlphaFold monomer V2.0 prediction for probable SERINE/THREONINE- protein kinase pkwa… · a predicted model of the same protein · chain B 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 P49695
- Elsewhere: RCSB PDB 5YZV · PDBe 5YZV · UniProt P49695
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